apply_filters: Filter gene counts matrix by applying various filters

In nkurniansyah/Olivia: RNA-seq Analysis

Filter gene counts matrix by applying various filters

Description

The purpose of filtering is to remove lowly express genes

Usage

apply_filters(
  count_matrix,
  median_min = 1,
  expression_sum_min = 10,
  max_min = 5,
  range_min = 5,
  prop_zero_max = 0.8,
  cv_min = NULL,
  cv_max = NULL,
  max_to_median_max = NULL
)

Arguments

count_matrix	A matrix of gene counts (possibly transformed). rows are genes, columns are individuals
median_min	minimum allowed median count value in the sample. Default is 1.
expression_sum_min	minimum allowed sum of counts across individuals. Default is 10.
max_min	minimum allowed maximum value in the sample for a gene. Default is 5.
range_min	minimum allowed range of counts in the sample. Default is 5.
prop_zero_max	maximum allowed proportion of individuals with count of zero for a transcript. Default is 0.8.
cv_min	minimum allowed value of coefficient of variation. Default is NULL.
cv_max	maximum allowed value of coefficient of variation. Default is NULL.
max_to_median_max	maximum allowed ratio between the maximum to the

Value

Matrix of gene counts, with filtered (reduced) rows.

Examples

data(rnaseq_count_matrix)

apply_filters(count_matrix=rnaseq_count_matrix, median_min = 1, expression_sum_min = 10,max_min = 5,
              range_min = 5, prop_zero_max = 0.8,cv_min = NULL, cv_max = NULL,
              max_to_median_max = NULL)

nkurniansyah/Olivia documentation built on July 29, 2023, 9:10 a.m.