deprecated: Deprecated functions
In stefanedwards/Siccuracy: Pipeline Package for AlphaImpute

Mostly renamed function names.

cbind_SNPs has been renamed to cbind_snp_files.

rowconcatenate has been renamed to cbind_snp_files.

imputation_accuracy1 and imputation_accuracy3 has been replaced by imputation_accuracy. The difference between the two former functions is now covered by the adaptive-argument of the latter.

mergeChips has been renamed to rbind_snp_files.

phasotogeno and phasotogeno_int have been replaced by convert_phases. The difference between the two former functions is covered by the int argument in the new function.

rbind_SNPs has been renamed to rbind_snp_files.

cbind_SNPs(fns, fnout, nlines, ncols, skiplines, excludeids, int)

rowconcatenate(fns, fnout, nlines = NULL, ncols = NULL, skiplines = 0,
  excludeids = integer(0))

imputation_accuracy3(truefn, imputefn, nSNPs = NULL, nAnimals = NULL,
  NAval = 9, standardized = TRUE)

imputation_accuracy1(truefn, imputefn, nSNPs = NULL, nAnimals = NULL,
  NAval = 9, standardized = TRUE)

mergeChips(hdid, ldid, hdpos, ldpos, hdfn, ldfn, fnout, outpos = NULL,
  missing = 9)

phasotogeno(phasefn, genofn, ncol = NULL, nrow = NULL)

phasotogeno_int(phasefn, genofn, ncol = NULL, nrow = NULL)

rbind_SNPs(hdid, ldid, hdpos, ldpos, hdfn, ldfn, fnout, outcol = NULL,
  na = 9, format = NULL, int = TRUE)

`fns`	Character vector of filenames to concatenate. Max 255 characters per filename due to R-Fortran.
`fnout`	Filename of resulting file
`nlines`	Number of lines to read from each file. When `NULL` (default), use all lines.
`ncols`	Number of columns to read from each file. When `NULL` (default), use all columns.
`skiplines`	Integer, number of lines to skip before outputting. `nlines` counts towards total number of lines, i.e. both skipped and outputted.
`excludeids`	Integer vector of first column id's to exclude from the output. `nlines` also counts towards excluded lines.
`int`	Logical (default `TRUE`), read and write integers.
`truefn, imputefn`	Deprected, was filename to files with true and imputed genotype matrix.
`nSNPs`	Deprecated, use `ncol`.
`nAnimals`	Deprecated, use `nlines`.
`NAval`	Deprecated, use `na`.
`standardized`	Logical, whether to center and scale genotypes by dataset in `true`-matrix. Currently by subtracting column mean and dividing by column standard deviation.
`hdid`	IDs of HD genotyped individuals. Corresponds to (subset of) first column of `hdfn`.
`ldid`	IDs of LD genotyped individuals. Corresponds to (subset of) first column of `ldfn`.
`hdpos`	Integer vector of where columns in `hdfn` are positioned in output file. Coerced to same length as columns in `hdfn`.
`ldpos`	Integer vector of where columns in `ldfn` are positioned in output file. Coerced to same length as columns in `ldfn`.
`hdfn`	Filename of HD genotypes.
`ldfn`	Filename of LD genotypes.
`outpos`	Integer vector of collective SNP positions. Default to sorted, union of `hdpos` and `ldpos`. Make it anything else and you get?
`missing`	Missing value.
`phasefn`	Filename of input file, every two rows are for same animal.
`genofn`	Filename of intended output.
`ncol`	Number of columns to read, if `NULL` (default), number is estimated from file.
`nrow`	Number of rows to maximally read from `phasefn`. If `NULL`, no limit is used.
`outcol`	Integer, number of columns in output file. When `NULL` (default), uses max value of `hdpos` and `ldpos`.
`na`	Value of missing genotypes.
`format`	Character, Fortran edit descriptors for output. See parseformat.