builds {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 = c("UCSC", "NCBI")) extractBuild(string, build = c("UCSC", "NCBI")) uniformBuilds(builds, cutoff = 0.2, na = c("", "NA"))
from |
character() A vector of build versions typically from 'genome()' (e.g., "37"). The build vector must be homogenous (i.e., 'length(unique(x)) == 1L'). |
to |
character(1) The name of the desired build version (either "UCSC" or "NCBI"; default: "UCSC") |
string |
A single character string |
build |
A vector of build version names (default UCSC, NCBI) |
builds |
A character vector of builds |
cutoff |
numeric(1L) An inclusive threshold tolerance value for missing values and translating builds that are below the threshold |
na |
character() The values to be considered as missing (default: c("", "NA")) |
translateBuild: A character vector of translated genome builds
extractBuild: A character string of the build information available
uniformBuilds: A character vector of builds where all builds are identical 'identical(length(unique(build)), 1L)'
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) navec <- c(rep(c("GRCh37", "hg19"), times = c(5, 1)), "NA") uniformBuilds(navec)