qpgraph_wrapper: Wrapper function around the original qpGraph program

In uqrmaie1/admixtools: Inferring demographic history from genetic data

Wrapper function around the original qpGraph program

Description

Wrapper function around the original qpGraph program

Usage

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

1. edges: data frame

2. score: scalar

3. f2: data frame

Examples

## Not run: 
qpgraph_wrapper('genotype_prefix', example_graph,
                 bin = 'path/to/qpGraph')

## End(Not run)

uqrmaie1/admixtools documentation built on Nov. 3, 2024, 12:56 a.m.