mergeCameraResults: Merge CAMERA results using limma default parameters and...

In bedapub/ribiosGSEA: Gene-Set Enrichment Analysis Tools in Ribios

Merge CAMERA results using limma default parameters and biosCamera parameters

Description

Merge CAMERA results using limma default parameters and biosCamera parameters

Usage

mergeCameraResults(
  matrix,
  index,
  designMatrix,
  contrast,
  featureLabels,
  weights = NULL,
  use.ranks = FALSE
)

Arguments

matrix	A numeric matrix, passed to camera and biosCamera
index	An index vector or a list of index vectors of features.
designMatrix	Design matrix.
contrast	A numeric vector of the same length as the number of columns in the design matrix, coefficients of contrasts.
featureLabels	A character vector of the same length as the number of rows of the matrix, feature labels, for instance gene symbols.
weights	NULL or numeric matrix of precision weights, passed to camera.
use.ranks	Logical, passed to camera. The function merges the output of camera with default options with the output of biosCamera, which appends additional information to camera methods, to return a comprehensive table as output.

See Also

camera, biosCamera

Examples

y <- matrix(rnorm(1000*6),1000,6)
features <- sprintf("Feature%d", 1:nrow(y))
design <- cbind(Intercept=1,Group=c(0,0,0,1,1,1))
# First set of 20 genes are genuinely deferentially expressed 
index1 <- 1:20
y[index1,4:6] <- y[index1,4:6]+1
# The second set of 20 genes are not
index2 <- 21:40
index1Res <- mergeCameraResults(y, index=index1, 
  designMatrix=design, contrast=c(0,1), featureLabels=features)
index1ListRes <- mergeCameraResults(y, index=list(index1), 
   designMatrix=design, contrast=c(0,1), featureLabels=features)
index12ListRes <- mergeCameraResults(y, index=list(index1, index2), 
   designMatrix=design, contrast=c(0,1), featureLabels=features)

bedapub/ribiosGSEA documentation built on March 30, 2023, 3:26 p.m.