translateBuild {TCGAutils} | R Documentation |
A few functions are available to search for build versions, either from NCBI or UCSC.
translateBuild
: translates between UCSC and NCBI build
versions
extractBuild
: use grep patterns to find the first build
within the string input
uniformBuilds
: replace build occurrences below a threshold
level of occurence with the alternative build
translateBuild(from, to = "UCSC") extractBuild(string, build = c("UCSC", "NCBI")) uniformBuilds(builds, cutoff = 0.2)
from |
A build version name |
to |
The name of the desired version |
string |
A single character string |
build |
A vector of build version names (default UCSC, NCBI) |
builds |
A character vector of builds |
cutoff |
A threshold value for translating builds below the threshold |
translateBuild("GRCh35", "UCSC") extractBuild( "SCENA_p_TCGAb29and30_SNP_N_GenomeWideSNP_6_G05_569110.nocnv_grch38.seg.txt" ) buildvec <- rep(c("GRCh37", "hg19"), times = c(5, 1)) uniformBuilds(buildvec)