twoGroupCountComparison: Compares the counts of two groups

In uzh/ezRun: An R meta-package for the analysis of Next Generation Sequencing Data

Compares the counts of two groups

Description

Compares the counts of two groups with the option to choose from several methods to test them.

Usage

twoGroupCountComparison(rawData)

runGfold(rawData, scalingFactors, isSample, isRef)

runDeseq2(
  x,
  sampleGroup,
  refGroup,
  grouping,
  grouping2 = NULL,
  isPresent = NULL,
  cooksCutoff = FALSE
)

runEdger(x, sampleGroup, refGroup, grouping, normMethod, priorCount = 0.125)

runGlm(
  x,
  sampleGroup,
  refGroup,
  grouping,
  normMethod,
  grouping2 = NULL,
  priorCount = 0.125,
  deTest = c("QL", "LR"),
  robust = FALSE
)

Arguments

rawData

a list of raw data obtained from loadCountDataset().

param

a list of parameters: testMethod defines the method to run: deseq2, exactTest, glm, sam or limma. Defaults to glm. grouping a character specifying the grouping. grouping2 a character vector specifying a secondary grouping. sampleGroup a character specifying the group to sample. refGroup a character specifying the reference group. normMethod a character specifying the normalization method for the edger and glm test methods. runGfold a logical indicating whether to run Gfold.

Value

Returns a list containing the results of the comparison.

Functions

• runGfold: Runs the Gfold test method.

• runDeseq2: Runs the Deseq2 test method.

• runEdger: Runs the EdgeR test method.

• runGlm: Runs the Glm test method.

Author(s)

Rehrauer, Hubert

Schmid, Peter

uzh/ezRun documentation built on Dec. 26, 2024, 9:53 a.m.