{ "cells": [ { "cell_type": "markdown", "id": "facial-pipeline", "metadata": {}, "source": [ "# Tutorial 7: Pancan data access\n", "\n", "This tutorial shows how to use the `cptac.pancan` submodule to access data from the harmonized pipelines for all cancer types.\n", "\n", "Before the harmonized pipelines, the team working on each cancer type had their own pipeline for each data type. So for example, the ccRCC team ran the ccRCC data through their own transcriptomics pipeline, and the HNSCC team ran the HNSCC data through a different transcriptomics pipeline. However, this made it hard to study trends across multiple cancer types, since each cancer type's data had been processed differently.\n", "\n", "To fix this problem, all data for all cancer types was run through the same pipelines for each data type. These are the harmonized pipelines. Now, for example, you can get transcriptomics data for both ccRCC and HNSCC (and all other cancer types) that came from the same pipeline.\n", "\n", "For some data types, multiple harmonized pipelines were available. In this cases, all cancers were run through each pipeline, and you can choose which one to use. For example, you can get transcriptomics data from either the BCM pipeline, the Broad pipeline, or the WashU pipeline. But whichever pipeline you choose, you can get transcriptomics data for all cancer types through that one pipeline.\n", "\n", "First, we'll import the package." ] }, { "cell_type": "code", "execution_count": 1, "id": "dress-rebate", "metadata": {}, "outputs": [], "source": [ "import cptac.pancan as pc" ] }, { "cell_type": "markdown", "id": "bb3d6f6b", "metadata": {}, "source": [ "We can list which cancers we have data for." ] }, { "cell_type": "code", "execution_count": 2, "id": "94d73be3", "metadata": {}, "outputs": [ { "name": "stdout", "output_type": "stream", "text": [ "PancanBrca\n", "PancanCcrcc\n", "PancanCoad\n", "PancanGbm\n", "PancanHnscc\n", "PancanLscc\n", "PancanLuad\n", "PancanOv\n", "PancanUcec\n", "PancanPdac\n" ] } ], "source": [ "pc.list_datasets()" ] }, { "cell_type": "markdown", "id": "distributed-impossible", "metadata": {}, "source": [ "## Download \n", "\n", "Authentication through your Box account is required when you download files. Pass the name of the dataset you want, as listed by `list_datasets`. Capitalization does not matter.\n", "\n", "See the end of this tutorial for how to download files on a remote computer that doesn't have a web browser for logging into Box." ] }, { "cell_type": "code", "execution_count": 3, "id": "national-sperm", "metadata": {}, "outputs": [ { "name": "stdout", "output_type": "stream", "text": [ "Please login to Box on the webpage that was just opened and grant access for cptac to download files through your account. If you accidentally closed the browser window, press Ctrl+C and call the download function again.\n", "Please login to Box on the webpage that was just opened and grant access for cptac to download files through your account. If you accidentally closed the browser window, press Ctrl+C and call the download function again.\n", " \r" ] }, { "data": { "text/plain": [ "True" ] }, "execution_count": 3, "metadata": {}, "output_type": "execute_result" } ], "source": [ "pc.download(\"pancanbrca\")" ] }, { "cell_type": "markdown", "id": "metropolitan-stranger", "metadata": {}, "source": [ "## Load the BRCA dataset" ] }, { "cell_type": "code", "execution_count": 4, "id": "compliant-rachel", "metadata": {}, "outputs": [ { "name": "stdout", "output_type": "stream", "text": [ "Loading broadbrca v1.0... \r" ] }, { "name": "stderr", "output_type": "stream", "text": [ "/home/caleb/anaconda3/envs/dev/lib/python3.9/site-packages/gtfparse/read_gtf.py:151: FutureWarning: The warn_bad_lines argument has been deprecated and will be removed in a future version.\n", "\n", "\n", " result = parse_gtf(\n", "/home/caleb/anaconda3/envs/dev/lib/python3.9/site-packages/gtfparse/read_gtf.py:151: FutureWarning: The error_bad_lines argument has been deprecated and will be removed in a future version.\n", "\n", "\n", " result = parse_gtf(\n" ] }, { "name": "stdout", "output_type": "stream", "text": [ " \r" ] } ], "source": [ "br = pc.PancanBrca()" ] }, { "cell_type": "markdown", "id": "05f6c2ae", "metadata": {}, "source": [ "We can list which data types are available from which sources." ] }, { "cell_type": "code", "execution_count": 5, "id": "dce3f8b3", "metadata": {}, "outputs": [ { "data": { "text/html": [ "
\n", "\n", "\n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", "
Data typeAvailable sources
0CNVwashu
1acetylproteomicspdc
2cancer_diagnosismssm
3clinicalmssm, pdc
4deconvolution_cibersortwashu
5deconvolution_xcellwashu
6demographicmssm
7followupmssm
8phosphoproteomicspdc, umich
9previous_cancermssm
10proteomicspdc, umich
11somatic_mutationharmonized, washu
12transcriptomicsbcm, broad, washu
13tumor_puritywashu
\n", "
" ], "text/plain": [ " Data type Available sources\n", "0 CNV washu\n", "1 acetylproteomics pdc\n", "2 cancer_diagnosis mssm\n", "3 clinical mssm, pdc\n", "4 deconvolution_cibersort washu\n", "5 deconvolution_xcell washu\n", "6 demographic mssm\n", "7 followup mssm\n", "8 phosphoproteomics pdc, umich\n", "9 previous_cancer mssm\n", "10 proteomics pdc, umich\n", "11 somatic_mutation harmonized, washu\n", "12 transcriptomics bcm, broad, washu\n", "13 tumor_purity washu" ] }, "execution_count": 5, "metadata": {}, "output_type": "execute_result" } ], "source": [ "br.list_data_sources()" ] }, { "cell_type": "markdown", "id": "ebaaa91f", "metadata": {}, "source": [ "Let's get some data tables." ] }, { "cell_type": "code", "execution_count": 6, "id": "gorgeous-extraction", "metadata": {}, "outputs": [ { "data": { "text/html": [ "
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Overall survialRecurrence status (1, yes; 0, no)Recurrence-free survivalSample_Tumor_NormalSurvial status (1, dead; 0, alive)baseline/ajcc_tnm_cancer_staging_editionbaseline/clinical_staging_distant_metastasisbaseline/he_staining_donebaseline/histologic_typebaseline/ihc_staining_done...medications/history_sourcemedications/medication_name_vitamins_supplementsprocurement/blood_collection_minimum_required_blood_collectedprocurement/blood_collection_number_of_blood_tubes_collectedprocurement/normal_adjacent_tissue_collection_number_of_normal_segments_collectedprocurement/tumor_tissue_collection_clamps_usedprocurement/tumor_tissue_collection_frozen_with_octprocurement/tumor_tissue_collection_number_of_tumor_segments_collectedprocurement/tumor_tissue_collection_tumor_typetumor_code
Patient_ID
01BR001421.00.0NaNTumor0.0NaNNaNNaNInflitrating Ductal CarcinomaNaN...NaNNaNNaN2.0NaNNaNNaNNaNNaNBR
01BR008NaNNaNNaNTumorNaNNaNNaNNaNNaNNaN...NaNNaNNaNNaNNaNNaNNaNNaNNaNNaN
01BR009NaNNaNNaNTumorNaNNaNNaNNaNNaNNaN...NaNNaNNaNNaNNaNNaNNaNNaNNaNNaN
01BR010NaNNaNNaNTumorNaNNaNNaNNaNNaNNaN...NaNNaNNaNNaNNaNNaNNaNNaNNaNNaN
01BR015347.00.0NaNTumor0.0NaNNaNNaNInflitrating Ductal CarcinomaNaN...NaNNaNNaN2.0NaNNaNNaNNaNNaNBR
01BR017413.00.0NaNTumor0.0NaNNaNNaNInflitrating Ductal CarcinomaNaN...NaNNaNNaN1.0NaNNaNNaNNaNNaNBR
01BR018384.00.0NaNTumor0.0NaNNaNNaNInflitrating Ductal CarcinomaNaN...NaNNaNNaN2.0NaNNaNNaNNaNNaNBR
01BR020NaNNaNNaNTumorNaNNaNNaNNaNNaNNaN...NaNNaNNaNNaNNaNNaNNaNNaNNaNNaN
01BR023NaNNaNNaNTumorNaNNaNNaNNaNNaNNaN...NaNNaNNaNNaNNaNNaNNaNNaNNaNNaN
01BR025601.00.0NaNTumor0.0NaNNaNNaNInflitrating Ductal CarcinomaNaN...NaNNaNNaN1.0NaNNaNNaNNaNNaNBR
01BR026NaN0.0NaNTumorNaNNaNNaNNaNNaNNaN...NaNNaNNaN2.0NaNNaNNaNNaNNaNBR
01BR027351.00.0NaNTumor0.0NaNNaNNaNInflitrating Ductal CarcinomaNaN...NaNNaNNaN2.0NaNNaNNaNNaNNaNBR
01BR028NaN0.0NaNTumorNaNNaNNaNNaNNaNNaN...NaNNaNNaN2.0NaNNaNNaNNaNNaNBR
01BR030389.00.0NaNTumor0.0NaNNaNNaNInflitrating Ductal CarcinomaNaN...NaNNaNNaN2.0NaNNaNNaNNaNNaNBR
01BR031363.00.0NaNTumor0.0NaNNaNNaNInflitrating Ductal CarcinomaNaN...NaNNaNNaN2.0NaNNaNNaNNaNNaNBR
01BR032363.00.0NaNTumor0.0NaNNaNNaNInflitrating Ductal CarcinomaNaN...NaNNaNNaN2.0NaNNaNNaNNaNNaNBR
01BR033351.00.0NaNTumor0.0NaNNaNNaNInflitrating Lobular CarcinomaNaN...NaNNaNNaN2.0NaNNaNNaNNaNNaNBR
01BR040NaN0.0NaNTumorNaNNaNNaNNaNInflitrating Ductal CarcinomaNaN...NaNNaNNaN1.0NaNNaNNaNNaNNaNBR
01BR042NaN0.0NaNTumorNaNNaNNaNNaNInflitrating Ductal CarcinomaNaN...NaNNaNNaN1.0NaNNaNNaNNaNNaNBR
01BR043NaN0.0NaNTumorNaNNaNNaNNaNOther (specify)NaN...NaNNaNNaN1.0NaNNaNNaNNaNNaNBR
01BR044NaNNaNNaNTumorNaNNaNNaNNaNNaNNaN...NaNNaNNaNNaNNaNNaNNaNNaNNaNNaN
03BR002365.00.0NaNTumor0.0NaNNaNNaNInflitrating Ductal CarcinomaNaN...NaNNaNNaN2.0NaNNaNNaNNaNNaNBR
03BR004358.00.0NaNTumor0.0NaNNaNNaNInflitrating Ductal CarcinomaNaN...NaNNaNNaN2.0NaNNaNNaNNaNNaNBR
03BR005304.00.0NaNTumor0.0NaNNaNNaNInflitrating Lobular CarcinomaNaN...NaNNaNNaN2.0NaNNaNNaNNaNNaNBR
03BR006NaN0.0NaNTumorNaNNaNNaNNaNNaNNaN...NaNNaNNaN2.0NaNNaNNaNNaNNaNBR
03BR009NaN0.0NaNTumorNaNNaNNaNNaNNaNNaN...NaNNaNNaN2.0NaNNaNNaNNaNNaNBR
03BR010357.00.0NaNTumor0.0NaNNaNNaNInflitrating Lobular CarcinomaNaN...NaNNaNNaN1.0NaNNaNNaNNaNNaNBR
03BR011NaN0.0NaNTumorNaNNaNNaNNaNNaNNaN...NaNNaNNaN2.0NaNNaNNaNNaNNaNBR
03BR012390.00.0NaNTumor0.0NaNNaNNaNInflitrating Ductal CarcinomaNaN...NaNNaNNaN2.0NaNNaNNaNNaNNaNBR
03BR013355.00.0NaNTumor0.0NaNNaNNaNIDC and DCISNaN...NaNNaNNaN2.0NaNNaNNaNNaNNaNBR
..................................................................
14BR014448.00.0NaNTumor0.0NaNNaNNaNInflitrating Ductal CarcinomaNaN...NaNNaNNaN2.0NaNNaNNaNNaNNaNBR
14BR020NaN0.0NaNTumorNaNNaNNaNNaNNaNNaN...NaNNaNNaN2.0NaNNaNNaNNaNNaNBR
15BR003344.00.0NaNTumor0.0NaNNaNNaNInflitrating Ductal CarcinomaNaN...NaNNaNNaN2.0NaNNaNNaNNaNNaNBR
16BR012478.00.0NaNTumor0.0NaNNaNNaNInflitrating Ductal CarcinomaNaN...NaNNaNNaN2.0NaNNaNNaNNaNNaNBR
18BR002431.00.0NaNTumor0.0NaNNaNNaNInflitrating Ductal CarcinomaNaN...NaNNaNNaN2.0NaNNaNNaNNaNNaNBR
18BR003426.00.0NaNTumor0.0NaNNaNNaNInflitrating Ductal CarcinomaNaN...NaNNaNNaN2.0NaNNaNNaNNaNNaNBR
18BR004426.00.0NaNTumor0.0NaNNaNNaNInfiltrating Ductal and Mucinous CarcinomaNaN...NaNNaNNaN2.0NaNNaNNaNNaNNaNBR
18BR006419.00.0NaNTumor0.0NaNNaNNaNInflitrating Ductal CarcinomaNaN...NaNNaNNaN2.0NaNNaNNaNNaNNaNBR
18BR007431.00.0NaNTumor0.0NaNNaNNaNInflitrating Ductal CarcinomaNaN...NaNNaNNaN2.0NaNNaNNaNNaNNaNBR
18BR009417.00.0NaNTumor0.0NaNNaNNaNInflitrating Ductal CarcinomaNaN...NaNNaNNaN2.0NaNNaNNaNNaNNaNBR
18BR010410.00.0NaNTumor0.0NaNNaNNaNInflitrating Ductal CarcinomaNaN...NaNNaNNaN2.0NaNNaNNaNNaNNaNBR
18BR016449.00.0NaNTumor0.0NaNNaNNaNInflitrating Ductal CarcinomaNaN...NaNNaNNaN2.0NaNNaNNaNNaNNaNBR
18BR017445.00.0NaNTumor0.0NaNNaNNaNInflitrating Ductal CarcinomaNaN...NaNNaNNaN2.0NaNNaNNaNNaNNaNBR
18BR019437.00.0NaNTumor0.0NaNNaNNaNInflitrating Ductal CarcinomaNaN...NaNNaNNaN2.0NaNNaNNaNNaNNaNBR
20BR00187.00.0NaNTumor0.0NaNNaNNaNInflitrating Ductal CarcinomaNaN...NaNNaNNaN2.0NaNNaNNaNNaNNaNBR
20BR0029.00.0NaNTumor0.0NaNNaNNaNInflitrating Ductal CarcinomaNaN...NaNNaNNaN2.0NaNNaNNaNNaNNaNBR
20BR005357.00.0NaNTumor0.0NaNNaNNaNInflitrating Ductal CarcinomaNaN...NaNNaNNaN2.0NaNNaNNaNNaNNaNBR
20BR006327.00.0NaNTumor0.0NaNNaNNaNInflitrating Ductal CarcinomaNaN...NaNNaNNaN2.0NaNNaNNaNNaNNaNBR
20BR007357.00.0NaNTumor0.0NaNNaNNaNInflitrating Ductal CarcinomaNaN...NaNNaNNaN2.0NaNNaNNaNNaNNaNBR
20BR008347.00.0NaNTumor0.0NaNNaNNaNinvasive ductal carcinoma with extensive high-...NaN...NaNNaNNaN2.0NaNNaNNaNNaNNaNBR
21BR001NaN0.0NaNTumorNaNNaNNaNNaNNaNNaN...NaNNaNNaN2.0NaNNaNNaNNaNNaNBR
21BR002NaN0.0NaNTumorNaNNaNNaNNaNNaNNaN...NaNNaNNaN2.0NaNNaNNaNNaNNaNBR
21BR003NaN0.0NaNTumorNaNNaNNaNNaNNaNNaN...NaNNaNNaN2.0NaNNaNNaNNaNNaNBR
21BR010327.00.0NaNTumor0.0NaNNaNNaNInflitrating Ductal CarcinomaNaN...NaNNaNNaN2.0NaNNaNNaNNaNNaNBR
22BR003NaN0.0NaNTumorNaNNaNNaNNaNNaNNaN...NaNNaNNaN2.0NaNNaNNaNNaNNaNBR
22BR005348.00.0NaNTumor0.0NaNNaNNaNMixed ductal and lobular featuresNaN...NaNNaNNaN2.0NaNNaNNaNNaNNaNBR
22BR006282.00.0NaNTumor1.0NaNNaNNaNInflitrating Ductal CarcinomaNaN...NaNNaNNaN2.0NaNNaNNaNNaNNaNBR
604NaNNaNNaNTumorNaNNaNNaNNaNNaNNaN...NaNNaNNaNNaNNaNNaNNaNNaNNaNNaN
CPT000814NaNNaNNaNTumorNaNNaNNaNNaNNaNNaN...NaNNaNNaNNaNNaNNaNNaNNaNNaNNaN
CPT001846NaNNaNNaNTumorNaNNaNNaNNaNNaNNaN...NaNNaNNaNNaNNaNNaNNaNNaNNaNNaN
\n", "

146 rows × 114 columns

\n", "
" ], "text/plain": [ " Overall survial Recurrence status (1, yes; 0, no) \\\n", "Patient_ID \n", "01BR001 421.0 0.0 \n", "01BR008 NaN NaN \n", "01BR009 NaN NaN \n", "01BR010 NaN NaN \n", "01BR015 347.0 0.0 \n", "01BR017 413.0 0.0 \n", "01BR018 384.0 0.0 \n", "01BR020 NaN NaN \n", "01BR023 NaN NaN \n", "01BR025 601.0 0.0 \n", "01BR026 NaN 0.0 \n", "01BR027 351.0 0.0 \n", "01BR028 NaN 0.0 \n", "01BR030 389.0 0.0 \n", "01BR031 363.0 0.0 \n", "01BR032 363.0 0.0 \n", "01BR033 351.0 0.0 \n", "01BR040 NaN 0.0 \n", "01BR042 NaN 0.0 \n", "01BR043 NaN 0.0 \n", "01BR044 NaN NaN \n", "03BR002 365.0 0.0 \n", "03BR004 358.0 0.0 \n", "03BR005 304.0 0.0 \n", "03BR006 NaN 0.0 \n", "03BR009 NaN 0.0 \n", "03BR010 357.0 0.0 \n", "03BR011 NaN 0.0 \n", "03BR012 390.0 0.0 \n", "03BR013 355.0 0.0 \n", "... ... ... \n", "14BR014 448.0 0.0 \n", "14BR020 NaN 0.0 \n", "15BR003 344.0 0.0 \n", "16BR012 478.0 0.0 \n", "18BR002 431.0 0.0 \n", "18BR003 426.0 0.0 \n", "18BR004 426.0 0.0 \n", "18BR006 419.0 0.0 \n", "18BR007 431.0 0.0 \n", "18BR009 417.0 0.0 \n", "18BR010 410.0 0.0 \n", "18BR016 449.0 0.0 \n", "18BR017 445.0 0.0 \n", "18BR019 437.0 0.0 \n", "20BR001 87.0 0.0 \n", "20BR002 9.0 0.0 \n", "20BR005 357.0 0.0 \n", "20BR006 327.0 0.0 \n", "20BR007 357.0 0.0 \n", "20BR008 347.0 0.0 \n", "21BR001 NaN 0.0 \n", "21BR002 NaN 0.0 \n", "21BR003 NaN 0.0 \n", "21BR010 327.0 0.0 \n", "22BR003 NaN 0.0 \n", "22BR005 348.0 0.0 \n", "22BR006 282.0 0.0 \n", "604 NaN NaN \n", "CPT000814 NaN NaN \n", "CPT001846 NaN NaN \n", "\n", " Recurrence-free survival Sample_Tumor_Normal \\\n", "Patient_ID \n", "01BR001 NaN Tumor \n", "01BR008 NaN Tumor \n", "01BR009 NaN Tumor \n", "01BR010 NaN Tumor \n", "01BR015 NaN Tumor \n", "01BR017 NaN Tumor \n", "01BR018 NaN Tumor \n", "01BR020 NaN Tumor \n", "01BR023 NaN Tumor \n", "01BR025 NaN Tumor \n", "01BR026 NaN Tumor \n", "01BR027 NaN Tumor \n", "01BR028 NaN Tumor \n", "01BR030 NaN Tumor \n", "01BR031 NaN Tumor \n", "01BR032 NaN Tumor \n", "01BR033 NaN Tumor \n", "01BR040 NaN Tumor \n", "01BR042 NaN Tumor \n", "01BR043 NaN Tumor \n", "01BR044 NaN Tumor \n", "03BR002 NaN Tumor \n", "03BR004 NaN Tumor \n", "03BR005 NaN Tumor \n", "03BR006 NaN Tumor \n", "03BR009 NaN Tumor \n", "03BR010 NaN Tumor \n", "03BR011 NaN Tumor \n", "03BR012 NaN Tumor \n", "03BR013 NaN Tumor \n", "... ... ... \n", "14BR014 NaN Tumor \n", "14BR020 NaN Tumor \n", "15BR003 NaN Tumor \n", "16BR012 NaN Tumor \n", "18BR002 NaN Tumor \n", "18BR003 NaN Tumor \n", "18BR004 NaN Tumor \n", "18BR006 NaN Tumor \n", "18BR007 NaN Tumor \n", "18BR009 NaN Tumor \n", "18BR010 NaN Tumor \n", "18BR016 NaN Tumor \n", "18BR017 NaN Tumor \n", "18BR019 NaN Tumor \n", "20BR001 NaN Tumor \n", "20BR002 NaN Tumor \n", "20BR005 NaN Tumor \n", "20BR006 NaN Tumor \n", "20BR007 NaN Tumor \n", "20BR008 NaN Tumor \n", "21BR001 NaN Tumor \n", "21BR002 NaN Tumor \n", "21BR003 NaN Tumor \n", "21BR010 NaN Tumor \n", "22BR003 NaN Tumor \n", "22BR005 NaN Tumor \n", "22BR006 NaN Tumor \n", "604 NaN Tumor \n", "CPT000814 NaN Tumor \n", "CPT001846 NaN Tumor \n", "\n", " Survial status (1, dead; 0, alive) \\\n", "Patient_ID \n", "01BR001 0.0 \n", "01BR008 NaN \n", "01BR009 NaN \n", "01BR010 NaN \n", "01BR015 0.0 \n", "01BR017 0.0 \n", "01BR018 0.0 \n", "01BR020 NaN \n", "01BR023 NaN \n", "01BR025 0.0 \n", "01BR026 NaN \n", "01BR027 0.0 \n", "01BR028 NaN \n", "01BR030 0.0 \n", "01BR031 0.0 \n", "01BR032 0.0 \n", "01BR033 0.0 \n", "01BR040 NaN \n", "01BR042 NaN \n", "01BR043 NaN \n", "01BR044 NaN \n", "03BR002 0.0 \n", "03BR004 0.0 \n", "03BR005 0.0 \n", "03BR006 NaN \n", "03BR009 NaN \n", "03BR010 0.0 \n", "03BR011 NaN \n", "03BR012 0.0 \n", "03BR013 0.0 \n", "... ... \n", "14BR014 0.0 \n", "14BR020 NaN \n", "15BR003 0.0 \n", "16BR012 0.0 \n", "18BR002 0.0 \n", "18BR003 0.0 \n", "18BR004 0.0 \n", "18BR006 0.0 \n", "18BR007 0.0 \n", "18BR009 0.0 \n", "18BR010 0.0 \n", "18BR016 0.0 \n", "18BR017 0.0 \n", "18BR019 0.0 \n", "20BR001 0.0 \n", "20BR002 0.0 \n", "20BR005 0.0 \n", "20BR006 0.0 \n", "20BR007 0.0 \n", "20BR008 0.0 \n", "21BR001 NaN \n", "21BR002 NaN \n", "21BR003 NaN \n", "21BR010 0.0 \n", "22BR003 NaN \n", "22BR005 0.0 \n", "22BR006 1.0 \n", "604 NaN \n", "CPT000814 NaN \n", "CPT001846 NaN \n", "\n", " baseline/ajcc_tnm_cancer_staging_edition \\\n", "Patient_ID \n", "01BR001 NaN \n", "01BR008 NaN \n", "01BR009 NaN \n", "01BR010 NaN \n", "01BR015 NaN \n", "01BR017 NaN \n", "01BR018 NaN \n", "01BR020 NaN \n", "01BR023 NaN \n", "01BR025 NaN \n", "01BR026 NaN \n", "01BR027 NaN \n", "01BR028 NaN \n", "01BR030 NaN \n", "01BR031 NaN \n", "01BR032 NaN \n", "01BR033 NaN \n", "01BR040 NaN \n", "01BR042 NaN \n", "01BR043 NaN \n", "01BR044 NaN \n", "03BR002 NaN \n", "03BR004 NaN \n", "03BR005 NaN \n", "03BR006 NaN \n", "03BR009 NaN \n", "03BR010 NaN \n", "03BR011 NaN \n", "03BR012 NaN \n", "03BR013 NaN \n", "... ... \n", "14BR014 NaN \n", "14BR020 NaN \n", "15BR003 NaN \n", "16BR012 NaN \n", "18BR002 NaN \n", "18BR003 NaN \n", "18BR004 NaN \n", "18BR006 NaN \n", "18BR007 NaN 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procurement/tumor_tissue_collection_frozen_with_oct \\\n", "Patient_ID \n", "01BR001 NaN \n", "01BR008 NaN \n", "01BR009 NaN \n", "01BR010 NaN \n", "01BR015 NaN \n", "01BR017 NaN \n", "01BR018 NaN \n", "01BR020 NaN \n", "01BR023 NaN \n", "01BR025 NaN \n", "01BR026 NaN \n", "01BR027 NaN \n", "01BR028 NaN \n", "01BR030 NaN \n", "01BR031 NaN \n", "01BR032 NaN \n", "01BR033 NaN \n", "01BR040 NaN \n", "01BR042 NaN \n", "01BR043 NaN \n", "01BR044 NaN \n", "03BR002 NaN \n", "03BR004 NaN \n", "03BR005 NaN \n", "03BR006 NaN \n", "03BR009 NaN \n", "03BR010 NaN \n", "03BR011 NaN \n", "03BR012 NaN \n", "03BR013 NaN \n", "... ... \n", "14BR014 NaN \n", "14BR020 NaN \n", "15BR003 NaN \n", "16BR012 NaN \n", "18BR002 NaN \n", "18BR003 NaN \n", "18BR004 NaN \n", "18BR006 NaN \n", "18BR007 NaN \n", "18BR009 NaN \n", "18BR010 NaN \n", "18BR016 NaN \n", "18BR017 NaN \n", "18BR019 NaN \n", "20BR001 NaN \n", "20BR002 NaN \n", "20BR005 NaN \n", "20BR006 NaN \n", "20BR007 NaN \n", "20BR008 NaN \n", "21BR001 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AA_MAFAFR_MAFALLELE_NUMAMR_MAFASN_MAFAlleleAmino_acidsBAM_FileBIOTYPECANONICAL...dbSNP_Val_Statusflanking_bpsn_alt_countn_depthn_ref_countt_alt_countt_deptht_ref_countvariant_idvariant_qual
Patient_ID
01BR001NaNNaN1NaNNaNTR/WNaNprotein_codingYES...NaNNaN0635635180878698..
01BR001NaNNaN1NaNNaNGR/GNaNprotein_codingYES...NaNNaN012112124311287..
01BR001NaNNaN1NaNNaNCL/RNaNprotein_codingYES...NaNNaN177277114713981251..
01BR001NaNNaN1NaNNaNCG/ANaNprotein_codingYES...NaNNaN0585887769..
01BR001NaNNaN1NaNNaNTLNaNprotein_codingYES...NaNNaN01271279135126rs1213708101.
01BR001NaNNaN1NaNNaNTH/LNaNprotein_codingYES...NaNNaN01261269138129rs1256101256.
01BR001NaNNaN1NaNNaNTE/KNaNprotein_codingYES...NaNNaN037537553432379rs750883732.
01BR001NaNNaN1NaNNaNCNaNNaNprotein_codingYES...NaNNaN029129142283241..
01BR001NaNNaN1NaNNaNAT/MNaNprotein_codingYES...NaNNaN0468468160526366rs1161996687.
01BR001NaNNaN1NaNNaNCE/ANaNprotein_codingYES...NaNNaN021021076250174..
01BR001NaNNaN1NaNNaNCGNaNprotein_codingYES...NaNNaN015115128169141..
01BR001NaNNaN1NaNNaNTA/TNaNprotein_codingYES...NaNNaN133032949594545rs560309203.
01BR001NaNNaN1NaNNaNTNaNNaNprotein_codingYES...NaNNaN013913912121109..
01BR001NaNNaN1NaNNaNTR/KNaNprotein_codingYES...NaNNaN048548531470439..
01BR001NaNNaN1NaNNaN-QLY/HNaNprotein_codingYES...NaNNaN033733762369307..
01BR001NaNNaN1NaNNaNGE/QNaNprotein_codingYES...NaNNaN011211211115104..
01BR001NaNNaN1NaNNaN-TE/TXNaNprotein_codingYES...NaNNaN126326241326285..
01BR001NaNNaN1NaNNaNTT/SNaNprotein_codingYES...NaNNaN026226241251210..
01BR001NaNNaN1NaNNaNAA/ENaNprotein_codingYES...NaNNaN017517543276233..
01BR001NaNNaN1NaNNaNTSNaNprotein_codingYES...NaNNaN08988987412451171rs1201078361.
01BR001NaNNaN1NaNNaNGANaNprotein_codingYES...NaNNaN02424168064rs6510794.
01BR001NaNNaN1NaNNaNTRNaNprotein_codingYES...NaNNaN07373129078rs1407723717.
01BR001NaNNaN1NaNNaNAPNaNprotein_codingYES...NaNNaN032832838324286rs780981846.
01BR001NaNNaN1NaNNaNAP/TNaNprotein_codingYES...NaNNaN020520548213165rs1272201183.
01BR001NaNNaN1NaNNaNCNaNNaNprotein_codingYES...NaNNaN0626213141128..
01BR001NaNNaN1NaNNaNTR/KNaNprotein_codingYES...NaNNaN0447447248561313rs587782329.
01BR001NaNNaN1NaNNaNAC/YNaNprotein_codingYES...NaNNaN030430442401359..
01BR001NaNNaN1NaNNaNTV/INaNprotein_codingYES...NaNNaN019119180280200rs1224064736.
01BR001NaNNaN1NaNNaNAENaNprotein_codingYES...NaNNaN088887117110..
01BR001NaNNaN1NaNNaNCTNaNprotein_codingYES...NaNNaN022922924377353..
..................................................................
CPT001846NaNNaN1NaNNaNAT/SNaNprotein_codingYES...NaNNaN024724742266224..
CPT001846NaNNaN1NaNNaNAGNaNprotein_codingYES...NaNNaN038138173406333..
CPT001846NaNNaN1NaNNaNAV/MNaNprotein_codingYES...NaNNaN047547579431352..
CPT001846NaNNaN1NaNNaNGLNaNprotein_codingYES...NaNNaN036436487383296..
CPT001846NaNNaN1NaNNaNTL/QNaNprotein_codingYES...NaNNaN020120150236186rs768381227.
CPT001846NaNNaN1NaNNaNGM/TNaNprotein_codingYES...NaNNaN0241241100221121..
CPT001846NaNNaN1NaNNaNTG/VNaNprotein_codingYES...NaNNaN026226217327310..
CPT001846NaNNaN1NaNNaNGP/ANaNprotein_codingYES...NaNNaN0262262125306181rs770728317.
CPT001846NaNNaN1NaNNaNCCTGATCG/GIRXNaNprotein_codingYES...NaNNaN0138138139380..
CPT001846NaNNaN1NaNNaNAANaNprotein_codingYES...NaNNaN017117144187143rs754356731.
CPT001846NaNNaN1NaNNaNAE/KNaNprotein_codingYES...NaNNaN05050235431rs121913273.
CPT001846NaNNaN1NaNNaNCP/ANaNprotein_codingYES...NaNNaN07171244420..
CPT001846NaNNaN1NaNNaNAA/SNaNprotein_codingYES...NaNNaN0676758176..
CPT001846NaNNaN1NaNNaNGF/VNaNprotein_codingYES...NaNNaN161461379598519..
CPT001846NaNNaN1NaNNaNAG/SNaNprotein_codingYES...NaNNaN044144175400325..
CPT001846NaNNaN1NaNNaNCV/GNaNprotein_codingYES...NaNNaN019719752228176..
CPT001846NaNNaN1NaNNaNAV/FNaNprotein_codingYES...NaNNaN0535354944..
CPT001846NaNNaN1NaNNaNAS/FNaNprotein_codingYES...NaNNaN022122144320276rs1458254257.
CPT001846NaNNaN1NaNNaNGS/CNaNprotein_codingYES...NaNNaN0327327194481287..
CPT001846NaNNaN1NaNNaNTQ/KNaNprotein_codingYES...NaNNaN01221222210987rs768036293.
CPT001846NaNNaN1NaNNaNTS/LNaNprotein_codingYES...NaNNaN08585610296rs754681331.
CPT001846NaNNaN1NaNNaNCS/PNaNprotein_codingYES...NaNNaN21551539156147..
CPT001846NaNNaN1NaNNaNAP/TNaNprotein_codingYES...NaNNaN1756755142892750..
CPT001846NaNNaN1NaNNaNGL/SNaNprotein_codingYES...NaNNaN06363114635..
CPT001846NaNNaN1NaNNaNGS/RNaNprotein_codingYES...NaNNaN045845836639603..
CPT001846NaNNaN1NaNNaNGV/GNaNprotein_codingYES...NaNNaN116416314022383..
CPT001846NaNNaN1NaNNaNGF/SNaNprotein_codingYES...NaNNaN01371371110897..
CPT001846NaNNaN1NaNNaNGL/FNaNprotein_codingYES...NaNNaN017317348162114..
CPT001846NaNNaN1NaNNaNANaNNaNprotein_codingYES...NaNNaN0117117408141..
CPT001846NaNNaN1NaNNaNTR/*NaNprotein_codingYES...NaNNaN086861910283rs766848205.
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125 rows × 12922 columns

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" ], "text/plain": [ "Name A1BG A2M A2ML1 \\\n", "Database_ID ENSP00000263100.2 ENSP00000323929.8 ENSP00000299698.7 \n", "Patient_ID \n", "01BR001 0.964219 0.712229 -1.838762 \n", "01BR008 -0.163783 0.222128 0.564935 \n", "01BR009 0.440711 1.305547 1.064684 \n", "01BR010 -0.210077 -0.476778 -2.153951 \n", "01BR015 0.512848 -0.108772 -2.024479 \n", "01BR017 0.411871 0.906319 0.196331 \n", "01BR018 0.778780 0.949798 0.481126 \n", "01BR020 -0.120716 -0.366892 -1.963831 \n", "01BR023 -0.210646 -0.762573 -2.833123 \n", "01BR025 -0.324954 -0.733043 -1.483728 \n", "01BR026 0.758481 1.202558 1.653796 \n", "01BR027 -0.070443 0.921279 2.812488 \n", "01BR030 0.835516 1.079948 -0.901783 \n", "01BR031 0.113994 0.251315 -0.237275 \n", "01BR032 -0.258722 -0.173205 -2.424880 \n", "01BR033 0.617279 0.128125 -1.386833 \n", "01BR040 0.378537 0.541975 2.637356 \n", "01BR042 0.171510 0.216926 1.394348 \n", "01BR043 0.595189 0.453230 -0.418072 \n", "03BR002 1.182908 0.941207 -2.690989 \n", "03BR004 0.145626 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0.003726 \n", "01BR009 0.053902 -0.094669 \n", "01BR010 0.587893 -0.060439 \n", "01BR015 0.713279 -0.451709 \n", "01BR017 0.285940 -0.214578 \n", "01BR018 -0.185218 -0.077110 \n", "01BR020 0.389254 -0.758983 \n", "01BR023 -0.575809 0.295687 \n", "01BR025 -0.068224 -0.205014 \n", "01BR026 0.517863 0.128842 \n", "01BR027 0.029359 -0.368683 \n", "01BR030 -0.168015 -0.060944 \n", "01BR031 0.224898 -0.096730 \n", "01BR032 -0.298960 0.102774 \n", "01BR033 0.875703 -0.087547 \n", "01BR040 -0.162427 -0.276820 \n", "01BR042 0.032498 -0.255296 \n", "01BR043 0.149001 0.029414 \n", "03BR002 0.404512 -0.317661 \n", "03BR004 0.057986 -0.065817 \n", "03BR005 0.227620 -0.431134 \n", "03BR006 0.174024 -0.038653 \n", "03BR010 -0.570344 0.372747 \n", "03BR011 0.094380 -0.065768 \n", "03BR013 0.570092 -0.348289 \n", "05BR001 0.795425 -0.126655 \n", "05BR003 0.253951 -0.373283 \n", "05BR004 -0.219558 -0.265384 \n", "05BR005 0.627781 0.144078 \n", "... ... ... \n", "11BR080 0.111017 0.066190 \n", "13BR009 0.240534 0.344202 \n", "14BR005 -0.682161 0.232695 \n", "14BR008 0.205897 -0.259954 \n", "14BR014 0.249707 -0.189992 \n", "15BR003 0.266207 -0.397428 \n", "16BR012 0.195464 0.091912 \n", "18BR002 0.924180 -0.193535 \n", "18BR003 -0.259831 0.357311 \n", "18BR004 0.217149 0.395750 \n", "18BR006 0.156836 -0.019004 \n", "18BR007 0.294441 -0.179817 \n", "18BR009 0.180738 -0.027323 \n", "18BR010 0.390230 -0.408085 \n", "18BR016 0.262367 0.223140 \n", "18BR017 0.262079 0.602037 \n", "18BR019 -0.121304 0.176465 \n", "20BR001 -0.079242 0.118703 \n", "20BR002 0.674991 -0.449550 \n", "20BR005 0.815944 -0.052306 \n", "20BR006 -0.137395 0.101712 \n", "20BR007 0.398295 -0.110038 \n", "20BR008 0.656304 -0.082643 \n", "21BR001 -0.188882 0.552700 \n", "21BR002 0.174700 0.093894 \n", "21BR010 0.313672 -0.097084 \n", "22BR005 0.068183 -0.065201 \n", "22BR006 0.772068 0.454654 \n", "CPT000814 -0.011471 -0.279161 \n", "CPT001846 1.723409 -0.188145 \n", "\n", "[125 rows x 12922 columns]" ] }, "execution_count": 8, "metadata": {}, "output_type": "execute_result" } ], "source": [ "br.get_proteomics(source=\"umich\")" ] }, { "cell_type": "markdown", "id": "4a8b43c8", "metadata": {}, "source": [ "## Box authentication for remote downloads\n", "\n", "Normally, when you download the `cptac.pancan` data files you're required to log into your Box account, as these files are not released publicly. However, there may be situations where the computer you're running your analysis on doesn't have a web browser you can use to log in to Box. For example, you may be running your code in a remotely hosted notebook (e.g. Google Colabs), or on a computer cluster that you access using ssh.\n", "\n", "In these situations, follow these steps to take care of Box authenication:\n", "1. On a computer where you do have access to a web browser to log in to Box, load the `cptac.pancan` module.\n", "2. Call the `cptac.pancan.get_box_token` function. This will return a temporary access token that gives permission to download files from Box with your credentials. The token expires 1 hour after it's created.\n", "3. On the remote computer, when you call the `cptac.pancan.download` function, copy and paste the access token you generated on your local machine into the `box_token` parameter of the function. The program will then be able to download the data files.\n", "\n", "Below is all the code you would need to call for this process on each machine. For security, we will not actually run it in this notebook.\n", "\n", "On your local machine:\n", "```\n", "import cptac.pancan as pc\n", "pc.get_box_token()\n", "```\n", "\n", "On the remote machine:\n", "```\n", "import cptac.pancan as pc\n", "pc.download(\"pancanbrca\", box_token=[INSERT TOKEN HERE])\n", "```" ] } ], "metadata": { "kernelspec": { "display_name": "Python 3 (ipykernel)", "language": "python", "name": "python3" }, "language_info": { "codemirror_mode": { "name": "ipython", "version": 3 }, "file_extension": ".py", "mimetype": "text/x-python", "name": "python", "nbconvert_exporter": "python", "pygments_lexer": "ipython3", "version": "3.9.7" } }, "nbformat": 4, "nbformat_minor": 5 }