measure_gene_stats: A function to perform gene-level test using a sgRNA-level...

In CB2: CRISPR Pooled Screen Analysis using Beta-Binomial Test

A function to perform gene-level test using a sgRNA-level statistics.

Description

A function to perform gene-level test using a sgRNA-level statistics.

Usage

measure_gene_stats(sgrna_stat, logFC_level = "sgRNA")

Arguments

sgrna_stat	A data frame created by ‘measure_sgrna_stats’
logFC_level	The level of ‘logFC’ value. It can be ‘gene’ or ‘sgRNA’.

Value

A table contains the gene-level test result, and the table contains these columns:

• ‘gene’: Theg gene name to be tested.

• ‘n_sgrna’: The number of sgRNA targets the gene in the library.

• ‘cpm_a’: The mean of CPM of sgRNAs within the first group.

• ‘cpm_b’: The mean of CPM of sgRNAs within the second group.

• ‘logFC’: The log fold change of the gene between two groups. Taking the mean of sgRNA ‘logFC’s is default, and ‘logFC' is calculated by 'log2(cpm_b+1) - log2(cpm_a+1)’ if ‘logFC_level’ parameter is set to ‘gene’.

• ‘p_ts’: The p-value indicates a difference between the two groups at the gene-level.

• ‘p_pa’: The p-value indicates enrichment of the first group at the gene-level.

• ‘p_pb’: The p-value indicates enrichment of the second group at the gene-level.

• ‘fdr_ts’: The adjusted P-value of ‘p_ts’.

• ‘fdr_pa’: The adjusted P-value of ‘p_pa’.

• ‘fdr_pb’: The adjusted P-value of ‘p_pb’.

Examples

data(Evers_CRISPRn_RT112)
measure_gene_stats(Evers_CRISPRn_RT112$sg_stat)

CB2 documentation built on Nov. 5, 2025, 6:49 p.m.