CB2 (version 1.3.4)

measure_gene_stats: 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

# NOT RUN {
data(Evers_CRISPRn_RT112)
measure_gene_stats(Evers_CRISPRn_RT112$sg_stat)

# }