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probs_doqtl_to_qtl2()cross2_ril_to_genril() for converting a cross2 object of type "riln" to one of type "genriln" for some n.Added function cross2_do_to_genail8() for converting a cross2 object of type "do" to one of type "genail8". Also present with the alias cross2_do_to_genail().
Removed LazyData field from DESCRIPTION file
nchar() in encode_geno() as it no longer works properly with data frames.Cosmetic changes to prepare for posting to CRAN:
Revise package title and description.
Revise multi-core tests to never use >2 cores, even locally
Revise example for write2csv to use R’s temporary directory
Fix link to DOQTL, which is no longer in bioconductor release
write2csv() now includes an argument row.names. If NULL or NA (the default), row names are not written. Otherwise, row names are included in the output, and this is taken to be the name of that column. (Implements Issue #19.)Have map_df_to_list() ensure that the positions in the output are numeric.
Add further tests of map_df_to_list()…the case marker_column=NULL plus having the wrong marker or position column name.
Fix bug for the case marker_column=NULL.
encode_geno() now gives a warning if any allele codes have >1 character. (Issue #16)
Added scan_qtl_to_qtl2() to convert scanone() output from R/qtl into the new R/qtl2 scan1() format.
Small changes to find_unique_geno(), count_unique_geno(), and find_consensus_geno() to allow input to be a data frame.
Enable multi-core calculatings (adding cores argument) to find_unique_geno(), count_unique_geno(), find_consensus_geno(), and encode_geno().
Added cbind_smother() for combining matrices, but “smothering” columns in the first matrix by those in the second matrix that have the same name. Uses qtl2::cbind_expand().
probs_qtl2_to_array() for converting an R/qtl2 genotype probabilities object (well, just the autosomal part) into a three-dimensional array. This is particularly for use in comparing two sets of genotype probabilities to look for sample mix-ups (e.g., with the R/lineup2 package.probs_qtl2_to_doqtl() for converting the calc_genoprob() output from the R/qtl2 format to a single big 3-dimensional array, for use with DOQTL.probs_doqtl_to_qtl2() so that the genotypes are reordered appropriately. Still not sure about X chromosome, though.probs_qtl_to_qtl2 for converting genotype probabilities from R/qtl to R/qtl2 format.overwrite argument to write2csv. If overwrite=TRUE, write over file if it exists; if overwrite=FALSE, stop with an error.encode_geno: convert inputs to matrices if necessary.probs_doqtl_to_qtl2 and scan_qtl2_to_qtl to deal with changes to R/qtl2 data structures in qtl2geno and qtl2scan. Each function now needs a map object, generally created by qtl2geno::insert_pseudomarkers().These binaries (installable software) and packages are in development.
They may not be fully stable and should be used with caution. We make no claims about them.