diff --git a/DESCRIPTION b/DESCRIPTION index 01e59b9..51f8bf2 100644 --- a/DESCRIPTION +++ b/DESCRIPTION @@ -3,7 +3,7 @@ Maintainer: Stefan Dentro License: GPL-3 Type: Package Title: Battenberg subclonal copy number caller -Version: 2.2.2 +Version: 2.2.3 Authors@R: c(person("David", "Wedge", role=c("aut"), email="dw9@sanger.ac.uk"), person("Peter", "Van Loo", role=c("aut")), person("Stefan","Dentro", email="sd11@sanger.ac.uk", role=c("aut", "cre")), diff --git a/NAMESPACE b/NAMESPACE index 0464662..dc386c5 100644 --- a/NAMESPACE +++ b/NAMESPACE @@ -19,11 +19,12 @@ export(getAlleleCounts) export(getBAFsAndLogRs) export(infer_gender_birdseed) export(parse.imputeinfofile) +export(read_table_generic) export(run.impute) export(runASCAT) export(run_clonal_ASCAT) export(segment.baf.phased) export(segment.baf.phased.sv) export(squaresplot) -export(read_table_generic) importFrom(RColorBrewer,brewer.pal) +importFrom(readr,read_table) diff --git a/man/read_table_generic.Rd b/man/read_table_generic.Rd new file mode 100644 index 0000000..6f3ca7f --- /dev/null +++ b/man/read_table_generic.Rd @@ -0,0 +1,31 @@ +% Generated by roxygen2 (4.1.1): do not edit by hand +% Please edit documentation in R/util.R +\name{read_table_generic} +\alias{read_table_generic} +\title{Generic reading function using the readr R package, tailored for reading in genomic data} +\usage{ +read_table_generic(file, header = T, row.names = F, stringsAsFactor = F, + sep = "\\t", chrom_col = 1, skip = 0) +} +\arguments{ +\item{file}{Filename of the file to read in} + +\item{header}{Whether the file contains a header (Default: TRUE)} + +\item{row.names}{Whether the file contains row names (Default: FALSE)} + +\item{stringsAsFactor}{Legacy parameter that is no longer used (Default: FALSE)} + +\item{sep}{Column separator (Default: \t)} + +\item{chrom_col}{The column number that contains chromosome denominations. This column will automatically be cast as a character. Should be counted including the row.names (Default: 1)} + +\item{skip}{The number of rows to skip before reading (Default: 0)} +} +\value{ +A data frame with contents of the file +} +\description{ +Generic reading function using the readr R package, tailored for reading in genomic data +} +