differentialAbundance: Differential abundance analysis

In davidcoffey/LymphoSeq: Analyze high-throughput sequencing of T and B cell receptors

Description

Use a Fisher exact test to calculate differential abdunance of each sequence in two samples and reports the log2 transformed fold change, P value and adjusted P value.

Usage

differentialAbundance(sample1, sample2, list,
  abundance = "estimatedNumberGenomes", type = "aminoAcid", q = 1,
  zero = 0.001, parallel = FALSE)

Arguments

sample1	A character vector indicating the name of the first sample in the list to be compared.
sample2	A character vector indicating the name of the second sample in the list to be compared.
list	A list of data frames consisting of antigen receptor sequences imported by the LymphoSeq function readImmunoSeq.
abundance	The input value for the Fisher exact test. "estimatedNumberGenomes" is recommend but "count" may also be used.
type	A character vector indicating whether "aminoAcid" or "nucleotide" sequences should be used. If "aminoAcid" is specified, then run productiveSeqs first.
q	A numeric value between 0.0 and 1.0 indicating the threshold Holms adjusted P value (also knowns as the false discovery rate or q value) to subset the results with. Any sequences with a q value greater than this value will not be shown.
zero	A numeric value to set all zero values to when calculating the log2 transformed fold change between samples 1 and 2. This does not apply to the p and q value calculations.
parallel	A boolean indicating wheter parallel processing should be used or not.

Value

Returns a data frame with columns corresponding to the frequency of the abudance measure in samples 1 and 2, the P value, Q value (Holms adjusted P value, also knowns as the false discovery rate), and log2 transformed fold change.

Examples

file.path <- system.file("extdata", "TCRB_sequencing", package = "LymphoSeq")

file.list <- readImmunoSeq(path = file.path)

productive.aa <- productiveSeq(file.list = file.list, aggregate = "aminoAcid")

differentialAbundance(list = productive.aa, sample1 = "TRB_Unsorted_949", 
                      sample2 = "TRB_Unsorted_1320", type = "aminoAcid", q = 0.01, 
                      zero = 0.001)

davidcoffey/LymphoSeq documentation built on Dec. 31, 2019, 9:52 p.m.