onemap-internal: Internal onemap functions

In bschiffthaler/BatchMap: Software for the Creation of High Density Linkage Maps in Outcrossing Species

Description

Functions from onemap not to be directly called by the user.

Usage

acum(w)
avoid.reverse(input)
adjust.rf.ril(r,type,expand)
check.linkage(i, s, cl, geno, st, max.rf, LOD)
codif.data(geno.in,segr.type.in,cross = c("outcross"))
comb(x,y)
comb.ger(f)
compare.outcross(input.seq, n.best, tol, verbose)
Cindex(order,r)
diplo(w, seq.num, seq.phases)
est_rf_out(geno, mrk, seg_type, nind, verbose)
generate_all(input.seq, p, ws)
generate_one(input.seq, p, ws, no_reverse)
generate.overlapping.batches(input.seq, size = 50, overlap = 15, silent = FALSE)
generate_rand(input.seq, p, ws, n, pref)
get.bins(geno, exact)
get_twopt_info(twopt, small, big)
get_mat_rf_out(input.seq, LOD = FALSE, max.rf = 0.5, min.LOD = 0, useC = FALSE)
get_vec_rf_out(input.seq, LOD, max.rf, min.LOD, acum)
perm.pars(v)
perm.tot(v)
phases(input.seq, LOD=0, max.rf=0.50)
predict_time(batches, ws, timings)
rem.amb.ph(M,w,seq.num)
return.geno(segr.type, link.phases)
ser.ord(r,i)
try.seq.outcross(input.seq, mrk, tol, pos, verbose)
## S3 method for class 'compare'
print(x, ...)
## S3 method for class 'onemap'
print(x, ...)
## S3 method for class 'onemap.bin'
print(x, ...)
## S3 method for class 'order'
print(x, ...)
## S3 method for class 'order'
print(x, ...)
## S3 method for class 'outcross'
print(x, ...)
## S3 method for class 'sequence'
print(x, ...)

Author(s)

Gabriel Rodrigues Alves Margarido and Marcelo Mollinari

bschiffthaler/BatchMap documentation built on Dec. 16, 2019, 2:22 a.m.