run_estimation: A function to perform a statistical test at a sgRNA-level,...

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

A function to perform a statistical test at a sgRNA-level, deprecated.

Description

A function to perform a statistical test at a sgRNA-level, deprecated.

Usage

run_estimation(
  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’.

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