CB2 (version 1.3.4)

measure_sgrna_stats: 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

# NOT RUN {
library(CB2)
data(Evers_CRISPRn_RT112)
measure_sgrna_stats(Evers_CRISPRn_RT112$count, Evers_CRISPRn_RT112$design, "before", "after")

# }