builds {TCGAutils}R Documentation

Utilities for working with build numbers

Description

A few functions are available to search for build versions, either from NCBI or UCSC.

Usage

translateBuild(from, to = c("UCSC", "NCBI"))

extractBuild(string, build = c("UCSC", "NCBI"))

uniformBuilds(builds, cutoff = 0.2, na = c("", "NA"))

Arguments

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"))

Value

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)'

Examples


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)


[Package TCGAutils version 1.6.2 Index]