saveMarkersLists: Save top N marker genes for each cluster into a format...

In PolinaPavlovich/CONCLUS: ScRNA-seq workflow CONCLUS - from CONsensus CLUSters to a meaningful CONCLUSion.

Description

The function takes the output files of conclus::rankGenes(), extracts top N markers and saves them into the first "geneName" column of the output table. The second column "clusters" contains the name of the corresponding cluster.

Usage

saveMarkersLists(experimentName, dataDirectory,
  inputDir = file.path(dataDirectory, "marker_genes"),
  outputDir = file.path(dataDirectory,
  paste0("marker_genes/markers_lists")), pattern = "genes.tsv",
  Ntop = 100)

Arguments

experimentName	name of the experiment which appears at the beginning of the file name (supposed to be the same for one experiment during the workflow).
dataDirectory	experiment directory (supposed to be the same for one experiment during the workflow).
inputDir	input directory, usually "marker_genes" created automatically after conclus::runCONCLUS().
outputDir	output directory.
pattern	a pattern of the input file names to take.
Ntop	number of top markers to take from each cluster.

Value

It saves files into the outputDir. The number of files is equal to the number of clusters.

PolinaPavlovich/CONCLUS documentation built on May 10, 2019, 2:42 p.m.