signature_generator_paper: signature_generator_paper() Function

In jyoh1248/MyoSignature: Myocarditis signature proejct

signature_generator_paper() Function

Description

This function generate PCA plots according to batch

Usage

signature_generator_paper(
  raw_counts,
  samples_metadata,
  design_formula,
  rankingFormula,
  covid_genes,
  random_genes,
  top25_genes_paper,
  outDIR,
  outputName,
  fileName,
  heatmap_anno,
  heatmap_anno_colori,
  colScale,
  colScale2,
  genesymbol,
  logTransform,
  DESeq2required,
  ranking_groups,
  colorvalue,
  blindRun = TRUE,
  batch = NULL
)

Arguments

raw_counts	: raw counts matrix
samples_metadata	: metadata where names of raw counts match with metadata
design_formula	: formula used for DESeq2 process
covid_genes	: vector of genes (symbols), 116 genes
random_genes	: vecotr of genes (symbols), 98 genes
outDIR	: out directory
outputName	: file Name for final Rdata file
fileName	: names added for each plots
heatmap_anno	: heatmap annotation
heatmap_anno_colori	: heatmap colors
colScale	: scale_fill_manual
colScale2	: scale_color_manual
genesymbol	: gene symbol in raw counts, "ensemble" or "symbols"
logTransform	: if needed to process log2(x+1) transformation
DESeq2required	: if needed to process DESeq2 normalisation
ranking_groups	: groups that is used to calculate ranking
colorvalue	: values of colors with ranking groups
blindRun	: no messages during DESeq2 process (default = TRUE)
batch	: batch = NULL if not, run batch correction with limma packages (Chip variable)

Value

normalised matrix

Examples

signature_generator_paper()

jyoh1248/MyoSignature documentation built on May 18, 2022, 12:37 a.m.