combine_gRNAs.RdCombines gRNAs that target the same site into a single "combined" gRNA via addition of the expression levels.
combine_gRNAs(gRNA_matrix, site_table)a gRNA-by-cell expression matrix; the row names should be gRNA IDs
a data frame with column names "site" and "gRNA_id". The "site" column should give the target site of each gRNA ID
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)
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.
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)