Recent Releases of vcfR
vcfR - vcfR 1.11.0
Released on CRAN 2020-06-05 * Now compatible with R 4.0.0 and dplyr 1.0.0
- R
Published by knausb over 5 years ago
vcfR - vcfR v1.10.0
vcfR 1.10.0
Released on CRAN 2020-02-06 * Handled deprecated "dplyr::verb_" function in vcfR2tidy * Omitted unused elipses from proc.chromR()
- R
Published by knausb about 6 years ago
vcfR - vcfR v1.9.0
Released on CRAN 2020-01-10
* Changed class(x) == "matrix" to inherited(x, "matrix")
* Changed license from GPL to GPL-3 (#144).
* extract.haps() reports the correct number of variants processed when verbose.
* The square brackets ([]) handle @gt slots with no samples.
* vcfR2loci() now has the option return.alleles = FALSE.
* vcfR2genind() now has the option retrun.alleles = FALSE.
* Error handling code moved into the C++ functions called by read.vcfR so that errors are thrown earlier when reading a VCF. read.vcfR no longer checks that a file is readable first, which solves issues sometimes seen with shared files. (Issue #109, reported and fixed by @NikNakk).
* extract.haps() did not include the parameter return.alleles = TRUE in it's call to extract.gt() in the haploid branch of the function. This parameter has now been added. This also affects vcfR2DNAbin() which calls this function.
* vcfR2genlight() includes the parameter ... to pass parameters to adegenet::df2genind().
* is.indel() returns logical vector to identify indels.
* gt.to.popsum now handles genotypes that include some, but not all, missing alleles.
- R
Published by knausb about 6 years ago
vcfR - v1.8.0
vcfR 1.8.0
Released on CRAN 2018-04-17
* Attempted to address CRAN's 'Note: break used in wrong context: no loop is visible' issue.
* .vcf_stats_gz() reports number of elements in header as well as the file's last line. This is used by read.vcfR() to check for poorly formed files.
* show method for vcfR now queries @fix instead of @gt.
* check_keys() checks key definitions in the meta section to make sure they are unique.
* freq_peak_plot() has parameter posUnits to adjust units of scatterplot.
* vcfR2migrate() manual discusses Unix and Windows line endings.
- R
Published by knausb almost 8 years ago
vcfR - v1.7.0
This version was released to coincide with the submission of a manuscript on the subject of the inference of copy number variation.
vcfR 1.7.0
Released on CRAN 2018-02-07.
* vcf_field_names() now delimts on KEY= of key/value pairs, allows commas to be used within value.
* read.vcfR() will download files when provided with a link.
* Added example data from the Variant Effect Predictor (vep) data(vep).
- R
Published by knausb about 8 years ago
vcfR - v1.6.0
vcfR 1.6.0
Released on CRAN 2017-12-08.
* vcfR2DNAbin() can include indels and maintains alignment.
* write.vcf() now handles tilde expansion.
* rePOS() attempts to create a non-overlapping coordinate system from POS and CHROM.
* vcfR2DNAbin() manages the asterisk allele.
* extract.indels() ignores GATK's proc.chromR().
* Created peak_to_ploid() to call peaks and calculate dfe from freq_peak() output.
* Created freq_peak_plot() to help visualize the output of freq_peak().
* .vcf_stats_gz now has nrows and skip parameters.
* removed .Call() statements to standardize style.
* Created vcfR2migrate() to output MigrateN format data.
* Addressed clang-UBSAN memory leak in freq_peak().
* Created pairwise_genetic_diff() to calculate pairwise differentiation.
- R
Published by knausb about 8 years ago
vcfR -
Released on CRAN 2017-05-18.
- Created
genetic_diff()to calculate fixation indicies. - Addressed symbol recognition NOTE: https://github.com/RcppCore/Rcpp/issues/636#issuecomment-280985661.
- Moved
pinfsc50.pngto tools. - Added
samplesparameter to vcfR method[. - Deprecated the parameters 'chrom.s' and 'chrom.e' of 'chromo()', please use 'xlim' instead.
- Added
length()method for chromR objects. [method throws warning if FORMAT is omitted.plot()for signature 'chromR' handles INFO column when its all NA.create.chrom()subsets to first chromosome when more than one is provided.- adegenet::nLoc(NULL) appears to generate an error when converting data types.
- R
Published by knausb almost 9 years ago
vcfR - v1.4.0
Released on CRAN 2017-01-07.
- masplit() converts '.' to NA.
- extract.indels() does not recognize NA as a deletion.
- Added parameter getINFO to getFIX() to suppress INFO column.
- CRAN brought to my attention that I have new memory access issues which have been addressed.
- R
Published by knausb about 9 years ago
vcfR - v1.3.0
vcfR 1.3.0
Released on CRAN 2016-12-08.
- extract.gt() no longer uses parameter allele.sep().
- Added more info to chromR show method.
- When annotation data include more than one chromosome in create.chromR() the data are subset to the first chromosome. Thank you Christian!
- added convertNA parameter to extract.gt() to allow preservation of VCF encoding of missing data. Thank you Thierry!
- added convertNA parameter to read.vcfR() to allow preservation of VCF encoding of missing data. Thank you Thierry!
- extract.haps omits gt.split and implements unphasedasNA
- gtsplit handles a mixture of phased and unphased data
- Added 'getters' for vcfR and chromR slots. Thanks Zhian!
- Created freq_peak() to find peaks in allele balance frequency data.
- Created masplit() to parse matrices contains delimited strings.
- Created ordisample() to ordinate sample information.
- extract.gt() can now use the ID column from the fix region for rownames.
- Created INFO2df() and metaINFO2df().
- Prof Brian Ripley made me aware of memory leaks reported by valgrind.
Conditional jump or move depends on uninitialised value(s) - writevcfbody file initialization issue resolved.
- R
Published by knausb about 9 years ago
vcfR - v1.2.0 dplyr 0.5.0 compatibility
vcfR2genind()greps genotypes containing a missing allele ('.') and sets to NA.- dplyr v0.5.0 broke some vcfR2tidy functionality. This functionality should be fixed in this release.
is_het()rapidly identifies heterozygotes.extract.info()scores missing elements as NA.
- R
Published by knausb over 9 years ago
vcfR - Accepted pending minor revisions
vcfR 1.1.0
Released on CRAN 2016-05-26.
This release includes the incorporation of suggestions made by reviewers of the manuscript submitted to Molecular Ecology Resources.
- added is.het() to identify heterozygotes in a matrix of genotypes.
- Fixed one-off error in vcfR2DNAbin where a variant one position beyond the locus would attempt to be included but threw an error.
- Added examples to VCF input and output.
- Added vcfR_test as lightweight test VCF data.
- Changed chromR@name to chromR@names for consistency with other R objects.
- Added AD_frequency calculates allele frequencies from matrices of AD data.
- read.vcfR() handles VCF data with no GT region (ala LoFreq).
- gt2alleles handles missing data ('.').
- read.vcfR() checks for and removes carriage returns (Windows).
- vcfR2DNAbin converts 'NA' to 'n' prior to conversion to DNAbin.
- chromR2vcfR implements use.mask.
- extract.gt() converts "." to NA.
- Added tidyr compatibility - thank you Eric Anderson!
- write.vcf() now uses mask = TRUE.
- maf() provides counts and frequency for the minor (or other) allele.
- create.chromR() now handles instances with no seq and the annotation position exceeds the greatest VCF POS.
- read.vcfR() now handles tilde expansion.
- addID() populates the non-missing values in the ID column of VCF data by concatenating the chromosome and position.
- R
Published by knausb over 9 years ago