calc_inefficient_gRNA_logfc: calc_inefficient_gRNA_logfc

In alex-kalinka-cruk/fgcQC: QC metric calculations for CRISPR screen data produced at the FGC

Description

Calculates the logFC difference for inefficient sgRNA PAM-proximal sequences relative to all guides (taking the median of each).

Usage

calc_inefficient_gRNA_logfc(logfc, library, col_suffix)

Arguments

logfc	A data frame of log2 fold change data for each sample in the study (samples as columns, gRNAs as rows) as generated by 'fgcQC::calc_log2_fold_change_gRNAs'.
library	A data frame containing the library file in which the first column gives the sgRNA sequence and the second column gives the sgRNA ID.
col_suffix	A character string providing a name to go at the end of the output column name (e.g. 'ctrl_plasmid').

Value

A data frame containing two columns: 'log2FC_GCC_diff' and 'log2FC_TT_diff'.

Author(s)

Alex T. Kalinka, [e-mail]

References

Graf, R. et al. (2019) sgRNA sequence motifs blocking efficient CRISPR/Cas9-mediated gene editing. Cell Rep 26: 1098-1103.

alex-kalinka-cruk/fgcQC documentation built on June 23, 2020, 9:05 p.m.