lowIntFilter: Apply low intensity filters to a DGEobj

Description Usage Arguments Value Examples

View source: R/lowIntFilter.R

Description

Takes a DGEobj as input and applies a combination of low intensity filters as specified by the user. 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

 1
 2
 3
 4
 5
 6
 7
 8
 9
10
lowIntFilter(
  dgeObj,
  countThreshold,
  zfpkmThreshold,
  fpkThreshold,
  tpmThreshold,
  sampleFraction = 0.5,
  geneLength,
  verbose = FALSE
)

Arguments

dgeObj

A DGEobj with RNA-Seq (counts) data (Required)

countThreshold

Genes below this threshold are removed (10 is recommended).

zfpkmThreshold

Genes below this threshold are removed. (-3.0 is recommended)

fpkThreshold

Genes below this threshold are removed. (5 is recommended)

tpmThreshold

Genes below this threshold are removed.

sampleFraction

The proportion of samples that must meet the thresholds (Default = 0.5). Range > 0 and <= 1.

geneLength

Vector of geneLengths for rows of dgeObj. Required for FPK and zFPKM filters, unless dgeObj is a DGEobj. If a DGEobj is supplied, geneLength is retrieved from the DGEobj, unless supplied by the geneLength argument.

verbose

Prints messages about the filtering process.

Value

Same class as input object with low intensity rows removed

Examples

 1
 2
 3
 4
 5
 6
 7
 8
 9
10
11
12
13
14
15
  myDGEobj <- readRDS(system.file("exampleObj.RDS", package = "DGEobj"))
  dim(myDGEobj)

  # Simple count threshold in at least 3/4ths the samples
  myDGEobj <- lowIntFilter(myDGEobj,
                           countThreshold = 10,
                           sampleFraction = 0.5)
  dim(myDGEobj)

  # Count and FPK thresholds
  myDGEobj <- lowIntFilter(myDGEobj,
                           countThreshold = 10,
                           fpkThreshold = 5,
                           sampleFraction = 0.5)
  dim(myDGEobj)

DGEobj.utils documentation built on April 28, 2021, 9:06 a.m.