mendelList: Mendelian Error Checking

In smgogarten/GWASTools: Tools for Genome Wide Association Studies

Mendelian Error Checking

Description

mendelList creates a "mendelList" object (a list of trios). mendelListAsDataFrame converts a "mendelList" object to a data frame.

Usage

mendelList(familyid, offspring, father, mother, sex, scanID)

mendelListAsDataFrame(mendel.list)

Arguments

familyid	A vector of family identifiers.
offspring	A vector of offspring subject identifiers.
father	A vector of father identifiers.
mother	A vector of mother identifiers.
sex	A vector to specify whether each subject is male "M" or female "F".
scanID	A vector of scanIDs indicating unique genotyping instances for the offspring vector. In the case of duplicate samples, the same offspring identifier may correspond to multiple scanID values.
mendel.list	An object of class "mendelList".

Details

The lengths of familyid, offspring, father, mother, sex, and scanID must all be identical. These vectors should include all genotyped samples, i.e., samples present in the father and mother vectors should also appear in the offspring vector if there are genotypes for these samples, and their unique scan IDs should be given in the scanID vector.

Identifiers may be character strings or integers, but not factors.

The "mendelList" object is required as input for the mendelErr function.

Value

mendelList returns a "mendelList" object. A "mendelList" object is a list of lists. The first level list is all the families. The second level list is offspring within families who have one or both parents genotyped. Within the second level are data.frame(s) with columns "offspring", "father", and "mother" which each contain the scanID for each member of the trio (a missing parent is denoted by -1). When replicates of the same offsping ID occur (duplicate scans for the same subject), this data.frame has multiple rows representing all combinations of scanIDs for that trio.

mendelListAsDataFrame returns a data.frame with variables "offspring", "father", and "mother" which each contain the scanID for each member of the trio (a missing parent is denoted by -1). This takes every data.frame from the "mendelList" object and puts them all into one large data frame. This can be easier to work with for certain analyses.

Author(s)

Xiuwen Zheng, Matthew P. Conomos

See Also

mendelErr

Examples

# data frame of sample information.  No factors!
dat <- data.frame(family=c(1,1,1,1,2,2,2), offspring=c("a","a","b","c","d","e","f"),
  father=c("b","b",0,0,"e",0,0), mother=c("c","c",0,0,"f",0,0),
  sex=c("M","M","M","F","F","M","F"), scanID=1:7,
  stringsAsFactors=FALSE)
dat

men.list <- mendelList(dat$family, dat$offspring, dat$father, dat$mother,
                       dat$sex, dat$scanID)
men.list

# If fathers and mothers do not have separate entries in each vector,
# mendelList returns a "NULL":
dat <- dat[c(1,5),]
dat
mendelList(dat$family, dat$offspring, dat$father, dat$mother,
           dat$sex, dat$scanID)

men.df <- mendelListAsDataFrame(men.list)
men.df

smgogarten/GWASTools documentation built on Nov. 10, 2024, 9:54 p.m.