Relabel the positions of mutations in the designated ID

Relabel the positions of mutations in the designated ID

Usage

relabelMutPositions(se, conversionTable, mutNameDelimiter = ".")

Arguments

se

SummarizedExperiment object, with row names of the form XX.AA.NNN, where XX is the name of the reference sequence, AA is the position of the mutated codon, and NNN is the mutated codon or amino acid. . is the delimiter, to be specified in the mutNameDelimiter argument. For rows corresponding to sequences with multiple mutated codons, the row names contain multiple names of the form above in a single string, separated by "_".

conversionTable

data.frame with at least three columns:

• seqname The reference sequence name (should match XX in the mutation name)

• position The codon position (should match AA in the mutation name)

• name The new name for the codon (will replace AA in the mutation name, if the reference sequence matches seqname)

mutNameDelimiter

The delimiter used in the mutation name (. above).

Value

A SummarizedExperiment object with modified row names.

Author

Charlotte Soneson

Examples

x <- readRDS(system.file("extdata", "GSE102901_cis_se.rds",
                         package = "mutscan"))
conversionTable <- data.frame(seqname = "f", position = 0:32) 
conversionTable$name = paste0((conversionTable$position - 1) %/% 7 + 1, 
                              c("", rep(letters[1:7], 6))[1:33])
out <- relabelMutPositions(x, conversionTable)