| measure_gene_stats {CB2} | R Documentation |
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)