add_scaled_counts_bulk.get_low_expressed {ppcseq}R Documentation

Drop lowly transcribed genes for TMM normalization

Description

Drop lowly transcribed genes for TMM normalization

Usage

add_scaled_counts_bulk.get_low_expressed(
  .data,
  .sample = sample,
  .transcript = transcript,
  .abundance = count,
  factor_of_interest = NULL,
  minimum_counts = 10,
  minimum_proportion = 0.7
)

Arguments

.data

A tibble

.sample

The name of the sample column

.transcript

The name of the transcript/gene column

.abundance

The name of the transcript/gene abundance column

factor_of_interest

The name of the column of the factor of interest

minimum_counts

A positive integer. Minimum counts required for at least some samples.

minimum_proportion

A real positive number between 0 and 1. It is the threshold of proportion of samples for each transcripts/genes that have to be characterised by a cmp bigger than the threshold to be included for scaling procedure.

Value

A tibble filtered


[Package ppcseq version 1.2.0 Index]