int_heatmap: Integrated heatmap

In Kan-E/rnaseqviewer: Toolkit for automated, systematic, and integrated RNA-seq DEG analysis

Integrated heatmap

Description

Integrated heatmap

Usage

int_heatmap(Count_matrix_dir, Gene_set, pre_zscoring = T)

Arguments

Count_matrix_dir	Directory including count matrix txt files
Gene_set	gene set txt file
pre_zscoring	z-scoring before integration of data set

References

R. Gentleman, V. Carey, W. Huber and F. Hahne (2021). genefilter: methods for filtering genes from high-throughput experiments. R package version 1.72.1.

Gu, Z. (2016) Complex heatmaps reveal patterns and correlations in multidimensional genomic data. Bioinformatics.

Examples

library(rnaseqviewer)

data(DEG_list)
dir.create("DEG_list")
write.table(DEG_list[1], file = "DEG_list/dataset1.txt", sep = "\t", quote = FALSE)
write.table(DEG_list[2], file = "DEG_list/dataset2.txt", sep = "\t", quote = FALSE)
vennd("DEG_list")

dir.create("count_list")
data(Row_count_data)
data(Row_count_data2)
write.table(Row_count_data, file = "count_list/data1.txt", sep = "\t", quote = FALSE)
write.table(Row_count_data2, file = "count_list/data2.txt", sep = "\t", quote = FALSE)

int_heatmap(Count_matrix_dir = "count_list",
            Gene_set = "DEG_list/group_lists/dataset1:dataset2.txt")

Kan-E/rnaseqviewer documentation built on May 30, 2022, 10:34 a.m.