Description Usage Arguments Value Author(s)
founderNs
calculates the number of founder genotypes
represented in the DSPR RILs at a given position.
1 | founderNs(peakChr, peakPos, design, phenotype.dat, id.col)
|
peakChr |
character vector of length one. Must be one of the major chromosome arms in the Drosophila genome ('X','2L','2R','3L',or '3R'). |
peakPos |
numeric vector of length one. A position in base pairs in the DSPR position list (every 10kb). |
design |
a character string. For inbred RIL designs: 'inbredA', 'inbredB'. For cross designs: AAcross, BBcross, or 'ABcross'. A and B refer to the pA and pB set of DSPR RILs. |
phenotype.dat |
|
id.col |
a character string identifying the name of the column containing unique ids for the samples. e.g. for an inbred design, the patRIL column can be used as the id. |
A named numeric vector consisting of the numbers of RILs
in the phenotype.dat data.frame
with each founder
genotype at the given position. A RIl is assigned a founder
genotype if the HMM probability is over 0.95. The number of RILs
with a heterozygous genotype and an uncertain genotype are also
returned.
Elizabeth King (kingeg@missouri.edu)
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