View source: R/convert.DOQTL.to.HAPPY.R
convert.full.DOQTL.array.to.HAPPY | R Documentation |
This function produces a HAPPY-format genome cache from a founder haplotype reconstruction 3D array. DO-QTL does not normally output this 3D array, but rather the dosages. However, this function requires the full probabilities, not the dosages.
convert.full.DOQTL.array.to.HAPPY(
full.array,
map,
map.locus_name.colname = "SNP_ID",
map.chr.colname = "Chr",
map.physical_dist.colname = "Mb_NCBI38",
map.genetic_dist.colname = "cM",
HAPPY.output.path,
remove.chr.from.chr = FALSE,
physical_dist.is.Mb = TRUE,
allele.labels = LETTERS[1:8],
chr = c(1:19, "X"),
diplotype.order = c("DOQTL", "CC", "qtl2")
)
full.array |
3D array that contains the founder probabilities. Should be dimension n x 36 x p, where n is the number of individuals and p is the number of loci. |
map |
The map file (which contains important information on the loci) loaded into R. |
map.locus_name.colname |
DEFAULT: "SNP_ID". The column name in the map data that corresponds to locus/marker names. |
map.chr.colname |
DEFAULT: "Chr". The column name in the map data that corresponds to chromosome. |
map.physical_dist.colname |
DEFAULT: "Mb_NCBI38". The column name in the map data that corresponds to physical position. |
map.genetic_dist.colname |
DEFAULT: "cM". The column name in the map data that corresponds to genetic position. |
HAPPY.output.path |
The path to a directory that will be created as the HAPPY-format genome cache. |
remove.chr.from.chr |
DEFAULT: FALSE. Option to remove "chr" from chromosome information. As in, change "chr1" to "1". The function expects chromosome information to not include "chr" as a prefix. |
physical_dist.is.Mb |
DEFAULT: TRUE. IF true, Mb will be converted to bp within the function. |
allele.labels |
DEFAULT: NULL. Allows for specification of founder labels different from what is in the DO-QTL output. The DEFAULT of NULL leads to using the labels from the DO-QTL output. |
chr |
DEFAULT: c(1:19, "X"). Allows for specification of the chromosomes. DEFAULT is all the chromosomes from the mouse. |
diplotype.order |
DEFAULT: "DOQTL". Specify the order of the diplotypes in the 3D array, so that the rotation to dosages is done correctly. |
convert.full.DOQTL.array.to.HAPPY()
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