write_bedwritten in Rcpp and thoroughly tested against
write_bederror message for invalid data, documentation.
read_*code, updated docs and tests.
read_fambug (used to require phenotypes to be integers, now can be double numbers).
read_plink! Now all Plink reading and writing operations are supported.
read_plinknow includes row and column names automatically.
read_bedaccepts either row and column names or just their numbers.
write_plinkchecks these row and column names against the BIM and FAM tables for consistency, if these are all present.
BEDMatrixin testing, since it leaves temporary files open and on Windows they do not get deleted and leave confusing error messages behind.
include <cerrno>to my cpp code.
write_phen, a phenotype format (very similar to Plink's FAM) used by GCTA and EMMAX.
write_plinkreturns the data it wrote, invisibly as a list. Most useful for auto-generated data.
tidy_kinshipto transform a square symmetric matrix into a long-format table that is easy to sort and add annotations to
write_grmto read and write GCTA's binary genetic relatedness matrix (GRM) format.
appendoption, for writing extremely large files in parts.
read_eigenvecto read and write Plink/GCTA eigenvector files.
count_lines, uses C++ code (via Rcpp) to count file lines extremely quickly. Intended for counting numbers of individuals (from FAM and equivalent files) or numbers of loci (from BIM and equivalent files) when these files are extremely large and no other information is needed from those files.
read_eigenvecadded Plink 2 support via
commentoption, which by default now treats data after
#as comments. This enables automatically parsing eigenvec files generated by Plink 2, whose header line starts with
#(this header is ignored). Previously, parsing Plink 2 eigenvec files generated warnings and resulted in the first row being an additional row with all
read_bedadded a missing file check in R code.
lfafork doesn't have function
read.bedanymore, previously the slowest and most memory-hungry competitor, which
genio::read_plinkwas being compared to.
geno_to_charto convert genotype numeric codes (allele dosages such as 0, 1, 2) into character codes such as 'A/A', 'A/G', 'G/G' (depending on locus).
write_matrix, intended for admixture inference data.
read_bed, which previously incorrectly stated that the numerical genotypes (allele dosages) counted alternative alleles (allele 2 in BIM table), whereas the truth is that they count reference alleles (allele 1).
count_linesnow returns value as integer instead of double (a very minor bug/annoyance fix).
lfafrom suggested packages (no connection anymore since
lfacomparison was removed from vignette in version 184.108.40.20600).
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