make_pattern_matrix: Create a matrix of the patterns between conditions

In bulkAnalyseR: Interactive Shiny App for Bulk Sequencing Data

Create a matrix of the patterns between conditions

Description

This function determines the patterns between different conditions of each gene. It should be applied to the output of calculate_condition_mean_sd_per_gene.

Usage

make_pattern_matrix(tbl, n_sd = 2)

Arguments

tbl	the output of calculate_condition_mean_sd_per_gene
n_sd	number of standard deviations from the mean to use to construct the intervals; default is 2

Value

A matrix of single character patterns between conditions. The last column is named pattern and is a concatenation of all other columns.

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)
patmat <- make_pattern_matrix(tbl)
patmat

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