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.