readPlinkOut: Read plink output files

In CollapsABEL: Generalized CDH (GCDH) Analysis

Description

Read plink output files

Usage

readPlinkOut(filename, ...)

Arguments

filename	Filenames of plink output files, see collenv$.plink_out_ext
...	passed to one of readAssoc, readQassoc, readLinear, readLogistic

Value

data.frame

Author(s)

Kaiyin Zhong, Fan Liu

Examples

## Not run: 
dat1 = readPlinkOut("assoc/mmp13.assoc")
dat2 =    readAssoc("assoc/mmp13.assoc")
all(na.omit(dat1 == dat2))
dat1 = readPlinkOut("assoc/mmp13.assoc", c("CHR", "SNP", "P", "OR"))
dat2 =    readAssoc("assoc/mmp13.assoc", c("CHR", "SNP", "P", "OR"))
all(na.omit(dat1 == dat2))
dat1 = readPlinkOut("assoc/mmp13.qassoc")
dat2 =   readQassoc("assoc/mmp13.qassoc")
all(na.omit(dat1 == dat2))
dat1 = readPlinkOut("assoc/mmp13.qassoc", c("CHR", "SNP", "P", "R2"))
dat2 =   readQassoc("assoc/mmp13.qassoc", c("CHR", "SNP", "P", "R2"))
all(na.omit(dat1 == dat2))

## End(Not run)

CollapsABEL documentation built on May 1, 2019, 7:28 p.m.