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.

run_estimation(
  sgcount,
  design,
  group_a,
  group_b,
  delim = "_",
  ge_id = NULL,
  sg_id = NULL
)

`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.

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’.