prot.p.adjust_protwise: Adjust P-values for Multiple Comparisons per Protein

In statOmics/MSqRob: Robust statistical inference for quantitative LC-MS proteomics

Adjust P-values for Multiple Comparisons per Protein

Description

Given matrix or a list of matrices with a column containing p-values and a contrast matrix, adds a column containing Holm-adjusted p-values correcting for the number of independent contrasts. This function can also be used to calculate the corrected p-values in the second stage when performing stage-wise testing.

Usage

prot.p.adjust_protwise(coefmatlist, L, method = "Holm", pcol = "pval",
  qname = "qval", stage2 = FALSE, significant_stage1 = NULL)

Arguments

coefmatlist	Either a matrix containing a column with p-values or a list of such matrices.
L	A contrast matrix with the parameter levels as rows and a column for each contrast.
method	Correction method. Can be abbreviated. Defaults to "Holm", which is currently the only available option.
pcol	A character string or numeric index indicating the column containing the p-values. Defaults to "pval".
qname	A character string indicating the name that will be given to the column containing the q-values. Defaults to "qval".
stage2	Set this to TRUE when using this function in the 2nd stage of a stage-wise test.
significant_stage1	Only used when stage2 = TRUE. This should be a character vector of protein identifiers that were retained in the first stage during stage-wise testing.

Value

Depending on the input, either a matrix or a list of matrices with an extra numeric column containing corrected p-values.

Examples

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statOmics/MSqRob documentation built on Dec. 8, 2022, 6 a.m.