Convert input data files to an object of haplohh-class.
data2haplohh(
hap_file,
map_file = NA,
min_perc_geno.hap = NA,
min_perc_geno.mrk = 100,
min_maf = NA,
chr.name = NA,
popsel = NA,
recode.allele = FALSE,
allele_coding = "12",
haplotype.in.columns = FALSE,
remove_multiple_markers = FALSE,
polarize_vcf = TRUE,
capitalize_AA = TRUE,
vcf_reader = "data.table",
position_scaling_factor = NA,
verbose = TRUE
)file containing haplotype data (see details below).
file containing map information (see details below).
threshold on percentage of missing data for haplotypes
(haplotypes with less than min_perc_geno.hap percent of markers genotyped are discarded). Default is NA,
hence no constraint.
threshold on percentage of missing data for markers (markers genotyped on less than
min_perc_geno.mrk percent of haplotypes are discarded). By default, min_perc_geno.mrk=100,
hence only fully genotyped markers are retained.
This value cannot be set to NA or zero.
threshold on the Minor Allele Frequency. Markers having a MAF lower than or equal to minmaf are discarded.
In case of multi-allelic markers the second-most frequent allele is referred to as minor allele.
Setting this value to zero eliminates monomorphic sites. Default is NA,
hence no constraint.
name of the chromosome considered (relevant if data for several chromosomes is contained in the haplotype or map file).
code of the population considered (relevant for fastPHASE output which can contain haplotypes from various populations).
*Deprecated*. logical. FALSE by default. TRUE forces parameter allele_coding to "map",
FALSE leaves it unchanged.
the allele coding provided by the user. Either "12" (default), "01", "map" or "none".
The option is irrelevant for vcf files and ms output.
logical. If TRUE, phased input haplotypes are assumed to be in columns (as produced
by the SHAPEIT2 program (O'Connell et al., 2014).
logical. If FALSE (default), conversion
stops, if multiple markers with the same chromosomal position are encountered.
If TRUE, duplicated markers are removed (all but the first marker with identical positions).
logical. Only of relevance for vcf files. If TRUE (default), tries to polarize
variants with help of the AA entry in the INFO field. Unpolarized alleles are discarded.
If FALSE, allele coding of vcf file is used unchanged as internal coding.
logical. Only of relevance for vcf files with ancestral allele information.
Low confidence ancestral alleles are usually coded by lower-case letters. If TRUE (default), these are
changed to upper case before the alleles of the sample are matched for polarization.
library used to read vcf. By default, low-level parsing is
performed using the generic package data.table. In order to read compressed files,
the package R.utils must be installed, too.
If the specialized package vcfR is available, set this parameter to "vcfR".
intended primarily for output of ms where positions lie in the interval [0,1]. These can be rescaled to sizes of typical markers in real data.
logical. If TRUE (default), report verbose progress.
The returned value is an object of haplohh-class.
Five haplotype input formats are supported:
a "standard format" with haplotypes in rows and markers in columns (with no header, but a haplotype ID/name in the first column).
a "transposed format" similar to the one produced by the phasing program SHAPEIT2 (O'Connell et al., 2014) in which haplotypes are in columns and markers in rows (with neither header nor marker IDs nor haplotype IDs).
output files from the fastPHASE program (Sheet and Stephens, 2006).
If haplotypes from several different population were phased simultaneously (-u fastPHASE option
was used), it is necessary to specify the population of interest by parameter popsel
(if this parameter is not or wrongly set, the error message will provide a list of
the population numbers contained in the file).
files in variant call format (vcf). No mapfile is needed is this case. If
the file contains several chromosomes, it is necessary to choose one by parameter
chr.name.
output of the simulation program 'ms'. No mapfile is needed in this case. If the file
contains several 'runs', a specific number has to be specified by the
parameter chr.name.
The "transposed format" has to be explicitly set while the other formats are recognized automatically.
The map file contains marker information in three, or, if it is used for polarization (see below), five columns:
marker name/id
chromosome
position (physical or genetic)
ancestral allele encoding
derived allele encoding
The markers must be in the same order as in the haplotype file. If
several chromosomes are represented in the map file, it is necessary to choose that
which corresponds to the haplotype file by parameter chr.name.
Haplotypes can be given either with alleles already coded as numbers (in two possible ways)
or with the actual alleles (e.g. nucleotides) which can be translated into numbers
either using the fourth and fifth column of the map file or by their alpha-numeric order.
Correspondingly, the parameter allele_coding has to be set to either "12",
"01", "map" or "none":
"12": 0 represents missing values, 1 the ancestral allele
and 2 (or higher integers) derived allele(s).
"01": NA or '.' (a point) represent missing values, 0 the
ancestral and 1 (or higher integers) derived allele(s).
"map": for each marker, the fourth column of the map file
defines the ancestral allele and the fifth column derived alleles.
In case of multiple derived alleles, they must be separated by commas without space.
Alleles in the haplotype file which do not appear in neither of the two columns
of the map file are regarded as missing values (NA).
"none": NA or '.' (a point) represent missing values, otherwise for each
marker the allele that comes first in alpha-numeric
order is coded by 0, the next by 1, etc. Evidently, this coding does not convey
any information about allele status as ancestral or derived, hence the alleles
cannot be regarded as polarized.
The information of allelic ancestry is exploited only in the frequency-bin-wise
standardization of iHS (see ihh2ihs). However, although ancestry status does
not figure in the formulas of the cross populations statistics
Rsb and XP-EHH, their values do depend on the assigned status.
The arguments min_perc_geno.hap,
min_perc_geno.mrk and min_maf are evaluated in this order.
Scheet P, Stephens M (2006) A fast and flexible statistical model for large-scale population genotype data: applications to inferring missing genotypes and haplotypic phase. Am J Hum Genet, 78, 629-644.
O'Connell J, Gurdasani D, Delaneau O, et al (2014) A general approach for haplotype phasing across the full spectrum of relatedness. PLoS Genet, 10, e1004234.
# NOT RUN {
#copy example files into the current working directory.
make.example.files()
#create object using a haplotype file in "standard format"
hap <- data2haplohh(hap_file = "bta12_cgu.hap",
map_file = "map.inp",
chr.name = 12,
allele_coding = "map")
#create object using fastPHASE output
hap <- data2haplohh(hap_file = "bta12_hapguess_switch.out",
map_file = "map.inp",
chr.name = 12,
popsel = 7,
allele_coding = "map")
#clean up demo files
remove.example.files()
# }
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