| measure_sgrna_stats {CB2} | R Documentation |
A function to perform a statistical test at a sgRNA-level
Description
A function to perform a statistical test at a sgRNA-level
Usage
measure_sgrna_stats(
sgcount,
design,
group_a,
group_b,
delim = "_",
ge_id = NULL,
sg_id = NULL
)
Arguments
sgcount |
This data frame contains read counts of sgRNAs for the samples. |
design |
This table contains study design. It has to contain 'group.' |
group_a |
The first group to be tested. |
group_b |
The second group to be tested. |
delim |
The delimiter between a gene name and a sgRNA ID. It will be used if only rownames contains sgRNA ID. |
ge_id |
The column name of the gene column. |
sg_id |
The column/columns of sgRNA identifiers. |
Value
A table contains the sgRNA-level test result, and the table contains these columns:
‘sgRNA’: The sgRNA identifier.
‘gene’: The gene is the target of the sgRNA
‘n_a’: The number of replicates of the first group.
‘n_b’: The number of replicates of the second group.
‘phat_a’: The proportion value of the sgRNA for the first group.
‘phat_b’: The proportion value of the sgRNA for the second group.
‘vhat_a’: The variance of the sgRNA for the first group.
‘vhat_b’: The variance of the sgRNA for the second group.
‘cpm_a’: The mean CPM of the sgRNA within the first group.
‘cpm_b’: The mean CPM of the sgRNA within the second group.
‘logFC’: The log fold change of sgRNA between two groups.
‘t_value’: The value for the t-statistics.
‘df’: The value of the degree of freedom, and will be used to calculate the p-value of the sgRNA.
‘p_ts’: The p-value indicates a difference between the two groups.
‘p_pa’: The p-value indicates enrichment of the first group.
‘p_pb’: The p-value indicates enrichment of the second group.
‘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
library(CB2)
data(Evers_CRISPRn_RT112)
measure_sgrna_stats(Evers_CRISPRn_RT112$count, Evers_CRISPRn_RT112$design, "before", "after")