RUV-handling: Create an expression set using EDASeq function

In cavei/cellCB: Cell City Band

Create an expression set using EDASeq function

Description

Create an expression set using EDASeq function

Create an expression set using EDASeq function

Compute empirically invariant genes

Compute residuals

Filter expression

Filter expression

Filter expression using RPKM

Compute RPKM from eset

Usage

createSet(obj)

createSeqExpressionSet(expression, annotation)

computeEmpiricalUnvariants(set, number = 5000, varName = "days")

computeResiduals(set)

filterExps(cell, condition, expr, annotations, rcFilter = NULL)

filterExpression(
  cell,
  condition,
  expr,
  annotations,
  rcFilter = NULL,
  atLeastIn = 1,
  unvariantNumber = 5000,
  varName = "days"
)

filterExpressionByRpkmMean(
  cell,
  condition,
  expr,
  annotations,
  rcFilter = NULL,
  atLeastIn = 1,
  rpkmMean = NULL,
  unvariantNumber = 5000,
  varName = "days",
  gene_length = "gene_length.txt"
)

computeRPKM(
  eset,
  gene_length = "../m38.p5-ensembl-91-renge-length/gene_length.txt"
)

Arguments

obj	a list with $e expression and $ann annotation
expression	expression data
annotation	annotation data
set	an expression set
number	the number of desired invariant genes
varName	the variable that set up the contrast to compute invariants; default "days"
cell	string for cell name (can be ALL or a vector)
condition	string for cell condition (can be a vector with more than one)
expr	data matrix
annotations	annotation data referred to the matrix
rcFilter	minimal read count accepted in atLeastIn samples
atLeastIn	default 1 sample
unvariantNumber	number of invariant genes; default 5000
rpkmMean	minimal RPKM row mean accepted to keep the row; NULL
gene_length	filename of file containg gene lengths
eset	expression set

Value

expression set (eset)

expression set (eset)

a vector of invariant gene

a vector residuals

a list with filtered expression, filtered annotation

a filtered eset and other details

a filtered eset and other details

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