do not check names, i.e. do not convert dashes into dots in the row a…

…nd column names when loading TSV genotype data

R/load.R

@@ -899,12 +899,17 @@ fn_simulate_data = function(n=100, l=1000, ploidy=2, n_alleles=2, min_depth=5, m
 #' Load genotype data as an allele frequency matrix
 #' 
 #' @param fname_geno filename of the genotype file
-#'  This may be in:
+#'  This may be in 1 of 3 formats:
 #'      - VCF format, 
 #'      - allele frequency table saved as a tab-delimited file with a header line and the first 3 columns refer to the
 #'          chromosome (chr), position (pos), and allele (allele),
 #'          with subsequent columns referring to the allele frequencies of a sample, entry or pool.
 #'          Names of the samples, entries, or pools in the header line can be any unique string of characters.
+#'      - Rds file containing a single numeric n samples x p loci-alleles matrix of allele frequencies with non-null row and column names.
+#'          Row names can be any string of characters which identify the sample or entry or pool names.
+#'          Column names need to be tab-delimited, where first element refers to the chromosome or scaffold name, 
+#'          the second should be numeric which refers to the position in the chromosome/scaffold, and 
+#'          subsequent elements are optional which may refer to the allele identifier and other identifiers.
 #' @param ploidy ploidy level which will generate genotype classes instead of continuous allele frequencies.
 #'  If NULL, then continuous allele frequencies and no binning or classification into genotype classes
 #'  will be performed (Default=NULL).
@@ -985,7 +990,7 @@ fn_load_genotype = function(fname_geno, ploidy=NULL, retain_minus_one_alleles_pe
             ########################################
             ### TSV: allele frequency table file ###
             ########################################
-            df = utils::read.delim(fname_geno, sep="\t", header=TRUE)
+            df = utils::read.delim(fname_geno, sep="\t", header=TRUE, check.names=FALSE)
             if (!((grepl("chr", colnames(df)[1], ignore.case=TRUE)) &
                   (grepl("pos", colnames(df)[2], ignore.case=TRUE)) &
                   (grepl("allele", colnames(df)[3], ignore.case=TRUE)))