runWithParametersRpkm: Run a RUV with parameters

In cavei/cellCB: Cell City Band

Run a RUV with parameters

Description

Run a RUV with parameters

Usage

runWithParametersRpkm(
  dataFile,
  annotationFile,
  cell,
  condition,
  runWithK = 1,
  runWithFormula = "~days + W_1",
  removeSamples = NULL,
  varName = "days",
  pADJ.thr = 0.05,
  logfcthr = 1.5,
  rcFilter = 100,
  atLeastIn = 2,
  rpkmMean = 3,
  clusterK = 9,
  gene_length = "gene_length.txt"
)

Arguments

dataFile	the name of the file that contains the expression dataset
annotationFile	the name of the file that contains annotations
cell	the cell sample name to pick
condition	the condition
runWithK	run RUV using k covariates
runWithFormula	a string coercible with as.formula
removeSamples	remove the listed samples
varName	the variable to used to evaluate unwanted variance
pADJ.thr	the thresholf for pvalue adjusted
logfcthr	absolute log fold change
rcFilter	filter expression for genes minimal rowCounts in atLeastIn samples
atLeastIn	filter expression for genes minimal rowCounts in atLeastIn samples
rpkmMean	filter expression for genes with an average rpkm of 3
clusterK	try clusterize according to k clusters
gene_length	filename of file containg gene lengths

Value

DEGSclusters, DEGS, esetRUV and cell.data

cavei/cellCB documentation built on Sept. 14, 2023, 8:15 a.m.