calculate_condition_mean_sd_per_gene: Calculate statistics for each gene of an expression matrix...

In bulkAnalyseR: Interactive Shiny App for Bulk Sequencing Data

Calculate statistics for each gene of an expression matrix given a grouping

Description

This function calculates the mean and standard deviation of the expression of each gene in an expression matrix, grouped by the conditions supplied.

Usage

calculate_condition_mean_sd_per_gene(expression.matrix, condition)

Arguments

expression.matrix	the expression matrix; rows correspond to genes and columns correspond to samples; usually preprocessed by preprocessExpressionMatrix; a list (of the same length as modality) can be provided if #' length(modality) > 1
condition	the condition to group the columns of the expression matrix by; must be a factor of the same length as ncol(expression.matrix)

Value

A tibble in long format, with the mean and standard deviation of each gene in each condition. The standard deviation is increased to the minimum value in the expression matrix (the noise threshold) if it is lower, in order to avoid sensitivity to small changes.

Examples

expression.matrix.preproc <- as.matrix(read.csv(
  system.file("extdata", "expression_matrix_preprocessed.csv", package = "bulkAnalyseR"), 
  row.names = 1
))[1:500,]

condition <- factor(rep(c("0h", "12h", "36h"), each = 2))
tbl <- calculate_condition_mean_sd_per_gene(expression.matrix.preproc[1:10, ], condition)
tbl

bulkAnalyseR documentation built on Dec. 28, 2022, 2:04 a.m.