Wrapper function around the original qpGraph program

qpgraph_wrapper(
  pref,
  graph,
  bin = "~np29/o2bin/qpGraph",
  parfile = NULL,
  outdir = ".",
  printonly = FALSE,
  badsnps = NULL,
  lambdascale = -1,
  inbreed = "NO",
  diag = 1e-04,
  blgsize = 0.05,
  outpop = "NULL",
  loadf3 = NULL,
  lsqmode = "NO",
  fstdmode = "NO",
  hires = "NO",
  forcezmode = "NO",
  zthresh = 0,
  allsnps = "NO",
  oldallsnps = "NO",
  doanalysis = "YES",
  bigiter = 100,
  initmix = 0,
  env = "",
  verbose = TRUE
)

Arguments

pref: Prefix of the packedancestrymap format genotype files.
graph: An admixture graph or qpGraph graph file
bin: Location of the qpGraph binary
parfile: qpGraph parameter file
outdir: Output directory
printonly: Should output be executed or the command just be printed?
badsnps: badsnps
lambdascale: lambdascale
inbreed: inbreed
diag: diag
blgsize: blgsize
outpop: outgroup population
loadf3: loadf3
lsqmode: least-squares mode. sets the offdiagonal elements of the block-jackknife covariance matrix to zero.
fstdmode: fstdmode
hires: hires
forcezmode: forcezmode
zthresh: zthresh
allsnps: allsnps
oldallsnps: oldallsnps
doanalysis: doanalysis
bigiter: bigiter
initmix: initmix
env: Export environmental variables. See examples.
verbose: Print progress updates

Value

A list with parsed qpGraph output

edges: data frame
score: scalar
f2: data frame

Examples

if (FALSE) {
qpgraph_wrapper('genotype_prefix', example_graph,
                 bin = 'path/to/qpGraph')
}