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)