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Differential expression analysis between two samples

Source: R/statFunctions.R
diffExpInd.Rd

This function compares the expression of a repertoire level between two samples. Log-ratios are calculated on the occurrence of a selected repertoire level between two compared samples, and differentially expressed genes/sequences are identified based on the user-defined log-ratio threshold.

Usage

diffExpInd(
  x,
  sampleNames = NULL,
  level = c("aaClone", "ntClone", "V", "J", "VJ", "ntCDR3", "aaCDR3"),
  scale = c("frequency", "count"),
  th = 1.5,
  remove.zeros = TRUE
)

Arguments

x

an object of class RepSeqExperiment

sampleNames

a vector of character with the sample_ids of the repertoires to drop from the RepSeqExperiment object.

level

a character specifying the repertoire level to be analyzed. Should be one of "aaClone","ntClone","aaCDR3","ntCDR3","V", "J",or "VJ".

scale

a character specifying the type of occurrence to take into account: "count" or "frequency".

th

the lof2FC threshold to be used

remove.zeros

a boolean indicating whether or not repertoire levels that are completely absent in one of the two compared samples should be to take into account in the calculation.

Value

a data frame containing the list of differentially expressed repertoire levels, their occurrence in both samples and their calculated log2FC.

Examples


data(RepSeqData)

diff_expression <- diffExpInd(RepSeqData, 
                              level="V", 
                              scale="frequency", 
                              sampleNames = c("tripod-30-813","tripod-30-815"), 
                              remove.zeros = FALSE)