markerCandidates: Write candidate marker genes to a file

In PavlidisLab/markerGeneProfile: Cell type marker gene profiles in whole tissue samples

Description

Writes candidate marker genes to a file along with other required information (fold change and silhouette coefficient) Selects candidates based on fold change to the median expression of other samples and a minimum expression in the cell type

Usage

markerCandidates(design, expression, outLoc, groupNames,
  regionNames = NULL, PMID = "PMID", rotate = NULL, cores = 1,
  debug = NULL, sampleName = "sampleName",
  replicates = "originalIndex", foldChangeThresh = 10,
  minimumExpression = 8, background = 6, regionHierarchy = NULL,
  geneID = "Gene.Symbol", seed = NULL)

Arguments

design	data.frame. Metadata for the samples.
expression	data.frame. Expression data for the samples. Gene names should be included as a column. Any other non expression data not be of type double
outLoc	Directory to save the candidate genes
groupNames	column of the design with cell type names. If multiple columns are provided, selection will be performed for each independently
regionNames	column of the design with region names. Multiple regions can be listed separated by commas
PMID	column of the design with pubmed identifiers. This is required to identify the samples coming from the same study
rotate	double. percentage of samples to be removed. 0.33 is used for the study
cores	Number of cores to use for paralellization
debug	Nothing to see here
sampleName	column of the design with sample names matching the column names of the expression data
replicates	column of the design that groups replicates
foldChangeThresh	minimum fold change required for selection
minimumExpression	minimum level of expression for a marker gene in its cell type
background	level of expression that should be considered as background level
regionHierarchy	hiearchy of regions.
seed	seed for random generation. if NULL will be set to random

PavlidisLab/markerGeneProfile documentation built on July 11, 2019, 11:42 p.m.