seqAlleleFreq: Get Allele Frequencies or Counts

In SeqArray: Data management of large-scale whole-genome sequence variant calls

Description

Calculates the allele frequencies or counts for reference or minor alleles.

Usage

seqAlleleFreq(gdsfile, ref.allele=0L, minor=FALSE, .progress=FALSE,
    parallel=seqGetParallel(), verbose=FALSE)
seqAlleleCount(gdsfile, ref.allele=0L, minor=FALSE, .progress=FALSE,
    parallel=seqGetParallel(), verbose=FALSE)

Arguments

gdsfile	a SeqVarGDSClass object
ref.allele	NULL, a single numeric value, a numeric vector or a character vector; see Value
minor	if TRUE, return minor allele frequency/count
.progress	[deprecated] if TRUE, show progress information
parallel	FALSE (serial processing), TRUE (multicore processing), numeric value or other value; parallel is passed to the argument cl in seqParallel, see seqParallel for more details.
verbose	if TRUE, show progress information

Details

If the gds node 'genotype/data' (integer genotypes) is not available, the node 'annotation/format/DS' (numeric genotype dosages for alternative alleles) will be used to calculate allele frequencies. At a site, it assumes 'annotation/format/DS' stores the dosage of the 1st alternative allele in the 1st column, 2nd alt. allele in the 2nd column if it is multi-allelic, and so on.

Value

If ref.allele=NULL, the function returns a list of allele frequencies/counts according to all allele per site. If ref.allele is a single numeric value (like 0L), it returns a numeric/integer vector for the specified allele (0L for the reference allele, 1L for the first alternative allele, etc). If ref.allele is a numeric vector, ref.allele specifies each allele per site. If ref.allele is a character vector, ref.allele specifies the desired allele for each site (e.g, ancestral allele for the derived allele frequency/count).

Author(s)

Xiuwen Zheng

See Also

seqNumAllele, seqMissing, seqParallel, seqGetParallel

Examples

# the GDS file
(gds.fn <- seqExampleFileName("gds"))

# display
f <- seqOpen(gds.fn)

# return a list
head(seqAlleleFreq(f, NULL, verbose=TRUE))

# return a numeric vector
summary(seqAlleleFreq(f, 0L, verbose=TRUE))

# return a numeric vector
summary(seqAlleleFreq(f, 0L, minor=TRUE, verbose=TRUE))

# return a numeric vector, AA is ancestral allele
AA <- seqGetData(f, "annotation/info/AA", .padNA=TRUE)
summary(seqAlleleFreq(f, AA))
summary(seqAlleleFreq(f, AA, minor=TRUE))

# allele counts
head(seqAlleleCount(f, NULL, verbose=TRUE))
head(seqAlleleCount(f, 0L, verbose=TRUE))
head(seqAlleleCount(f, 0L, minor=TRUE, verbose=TRUE))
head(seqAlleleCount(f, AA, verbose=TRUE))
head(seqAlleleCount(f, AA, minor=TRUE, verbose=TRUE))

# close the GDS file
seqClose(f)

Example output

Loading required package: gdsfmt
[1] "/usr/lib/R/site-library/SeqArray/extdata/CEU_Exon.gds"

[..................................................]  0%, ETC: ---    
[==================================================] 100%, completed, 0s
[[1]]
[1] 0.96491228 0.03508772

[[2]]
[1] 0.990566038 0.009433962

[[3]]
[1] 0.96103896 0.03896104

[[4]]
[1] 0.1232877 0.8767123

[[5]]
[1] 0.92696629 0.07303371

[[6]]
[1] 0.994382022 0.005617978


[..................................................]  0%, ETC: ---    
[==================================================] 100%, completed, 0s
   Min. 1st Qu.  Median    Mean 3rd Qu.    Max. 
 0.0000  0.8114  0.9719  0.8488  0.9942  1.0000 

[..................................................]  0%, ETC: ---    
[==================================================] 100%, completed, 0s
    Min.  1st Qu.   Median     Mean  3rd Qu.     Max. 
0.000000 0.005731 0.027778 0.099848 0.155623 0.500000 
   Min. 1st Qu.  Median    Mean 3rd Qu.    Max.    NA's 
0.00556 0.80907 0.97222 0.84647 0.99427 1.00000      32 
   Min. 1st Qu.  Median    Mean 3rd Qu.    Max.    NA's 
0.00000 0.00568 0.02778 0.09892 0.15212 0.50000      32 

[..................................................]  0%, ETC: ---    
[==================================================] 100%, completed, 0s
[[1]]
[1] 110   4

[[2]]
[1] 105   1

[[3]]
[1] 148   6

[[4]]
[1]  18 128

[[5]]
[1] 165  13

[[6]]
[1] 177   1


[..................................................]  0%, ETC: ---    
[==================================================] 100%, completed, 0s
[1] 110 105 148  18 165 177

[..................................................]  0%, ETC: ---    
[==================================================] 100%, completed, 0s
[1]  4  1  6 18 13  1

[..................................................]  0%, ETC: ---    
[==================================================] 100%, completed, 0s
[1] 110 105   6 128 165 177

[..................................................]  0%, ETC: ---    
[==================================================] 100%, completed, 0s
[1]  4  1  6 18 13  1

SeqArray documentation built on Nov. 8, 2020, 5:08 p.m.