Description Usage Arguments Details Value Raw Alleles and Genotypes Enumerated Alleles/Genotypes Founder Alleles and Genotypes See Also
This function reads SNP genotype data from one or more VCF files, and
returns these as an R/qtl cross
geno
object.
1 | readGenoVCF(..., samples, founders = NULL, alleles = NULL)
|
... |
Input VCF file paths. |
samples |
Cross sample IDs. |
founders |
Founder sample IDs. |
alleles |
Mapping of founder sample IDs to founder allele symbols. |
If no founder samples are specified, this function assigns enumerated
genotypes at each locus according to the observed raw SNP genotype. So
for example, if the raw SNP alleles at a given locus are 'A'
and
'C'
, samples are assigned the genotypes '1'
and '2'
,
respectively.
If founder samples are specified, this function assigns to each marker a genotype symbol consisting of alleles that each correspond to a specific founder.
If the alleles
parameter is specified, this must be a mapping of
founder sample IDs to allele symbols (e.g.
mapping( c(DBVPG6044 = 'W', Y12 = 'S') )
). If the alleles
parameter is not specified, allele symbols are taken from the letters of the
alphabet (i.e. 'A'
, 'B'
etc.).
An R/qtl cross
geno
object.
A raw allele is the original marker value. Single-nucleotide variants (i.e.
'A'
, 'C'
, 'G'
, or 'T'
) are commonly used, and
are the only kind of marker supported by the shmootl package. These
must be converted into another kind of allele before doing QTL analysis.
For a given ploidy N
, a raw genotype is the concatenation of the set
of N
raw alleles. For example, given two 'A'
alleles at a
homozygous diploid marker, the genotype is 'AA'
.
An enumerated allele/genotype is a number representing the order of
occurrence of raw or founder genotypes at a specific marker (e.g. '1'
for the first observed allele, '2'
for the second). Enumerated alleles
and genotypes are identical, regardless of ploidy. The process of enumerating
genotypes is done independently for each marker, so a given enumerated
genotype does not have the same meaning across markers.
A founder allele is a single letter corresponding to a specific founder
strain, indicating that the region containing the marker derives from that
founder. For example, 'W'
might be used to represent the Western
Africa founder strain DBVPG6044
, or 'S'
might be used for
the Sake strain Y12
).
For a given ploidy N
, a founder genotype is the concatenation of the
set of N
founder alleles. For example, given one founder allele
'W'
and another 'S'
, the founder genotype is 'WS'
.
Other VCF functions: getSamplesVCF
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