Upping version number for release v2.2.3

DESCRIPTION

@@ -3,7 +3,7 @@ Maintainer: Stefan Dentro <sd11@sanger.ac.uk>
 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")),

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)

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
+}
+