prep_bthin_matrix_diffrep: prep_bthin_matrix_diffrep

In alextkalinka/delboy: Differential-representation analysis by Elastic-net Logistic regression with BinOmial-thinning validitY tests

Description

Prepare the matrix output from seqgendiff::thin_diff for use in differential representation analyses by, for example, DESeq2 or delboy.

Usage

prep_bthin_matrix_diffrep(
  data,
  bthin_matrix,
  sample_names,
  treat_cols,
  gene_column
)

Arguments

data	A data frame of normalized (and batch-corrected, if necessary) counts for a set of samples with the true signal controlled (by, for example, batch-correcting it).
bthin_matrix	The matrix output from seqgendiff::thin_diff.
sample_names	A character vector giving the sample names from the original input data provided to seqgendiff::thin_diff in their original order.
treat_cols	A vector of 1/0 where a 1 indicates a treatment sample in seqgendiff::thin_diff.
gene_column	A character string naming the column containing gene names.

Value

A data frame.

alextkalinka/delboy documentation built on Feb. 2, 2022, 4:19 p.m.