# Combine gRNAs

`combine_gRNAs.Rd`

Combines gRNAs that target the same site into a single "combined" gRNA via addition of the expression levels.

    combine_gRNAs(gRNA_matrix, site_table)

## Arguments

gRNA_matrix

  a gRNA-by-cell expression matrix; the row names should be gRNA IDs

site_table

  a data frame with column names "site" and "gRNA_id". The "site" column should give the target site of each gRNA ID

## Value

a "collapsed" gRNA-by-cell expression matrix, where gRNAs that target the same site have been collapsed into a single row (via addition of the constituent gRNAs)

## Details

Combining gRNAs that target the same site helps to increase statistical power. This operation is especially appealing when gRNA expression levels are low or there are not a lot of (e.g., < 100,000) cells.

## Examples

    library(magrittr)
    library(Matrix)
    library(dplyr)
    #>
    #> Attaching package: ‘dplyr’
    #> The following objects are masked from ‘package:stats’:
    #>
    #>     filter, lag
    #> The following objects are masked from ‘package:base’:
    #>
    #>     intersect, setdiff, setequal, union

    # 1. First example
    data(gRNA_matrix)
    data(site_table)
    combined_gRNA_matrix <- combine_gRNAs(gRNA_matrix, site_table)

    # 2. Second example
    # Here we group only the gRNAs that target sites "chr10:17457016-17457416"
    # and "chr18:48566684-48567084;" all others remain ungrouped
    site_table_2 <- site_table %>%
    filter(site %in% c("chr10:17457016-17457416", "chr18:48566684-48567084"))
    combined_gRNA_matrix_2 <- combine_gRNAs(gRNA_matrix, site_table_2)