lowIntFilter: Function lowIntFilter

In jrthompson54/DGE.Tools2: A function library to facilitate Differential Gene Expression Analysis

Description

Takes a DGEobj as input and applies a combination of low intensity filters. raw count, zFPKM, TPM and/or FPK filters are supported. A gene must pass all active filters. Not setting a threshold argument inactivates that threshold.

Usage

lowIntFilter(
  x,
  zfpkmThreshold,
  fpkThreshold,
  countThreshold,
  tpmThreshold,
  sampleFraction = 0.5,
  genelength = NULL,
  verbose = FALSE
)

Arguments

x	A DGEobj with RNA-Seq (counts) data (required).
zfpkmThreshold	Genes below this threshold are removed (-3.0 is recommended)
fpkThreshold	Genes below this threshold are removed (recommend 5).
countThreshold	Genes below this threshold are removed (recommend 10). Set to 0 to disable this filter.
tpmThreshold	Genes below this threshold are removed (tpm is supported by request, but FPK is a better length-normalized value to use as a filter)
sampleFraction	The proportion of samples that must meet the thresholds (Default = 0.5). Range >0 and <=1.
genelength	Vector of genelengths for rows of x. Required for FPK and zFPKM filters, unless x is a DGEobj. If a DGEobj is supplied, genelength is retrieved from the DGEobj, unless supplied by the genelength argument.
verbose	Prints some messages about the filtering process.

Value

Same class as input object with low intensity rows removed

Author(s)

John Thompson, [e-mail]

Examples

  #simple count threshold
  myDgeObj  = lowIntFilter (myDgeObj, countThreshold=10)

  #count and zFPKM thresholds
  myDgeObj  = lowIntFilter (myDgeObj, countThreshold=10, zfpkmThreshold = -3.0)

jrthompson54/DGE.Tools2 documentation built on May 12, 2021, 8:47 p.m.