getMetaData: Constructor for metadata

Description Usage Arguments Value Examples

View source: R/getMetaData.R

Description

This function allows constructor of phenotype information necessary for downstream analysis. See format of required fields. Function will also rearrange the rows such that trios are grouped together - with proband first, mother second, and father third.

Usage

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getMetaData(path, id = "subj_id", familyId = "family_id",
  fatherId = "father_id", motherId = "mother_id", bamPath = "bam_path")

Arguments

path

The path pointing to the file that contains information on each subject in the dataset.

id

The column name that identifies each sample. Defaults to 'subj_id'.

familyId

The column name that identifies which family the sample belongs to. Defaults to 'family_id'.

fatherId

The column name that identifies the id of the father. Defaults to 'father_id'.

motherId

The column name that identifies the id of the mother. Defaults to 'mother_id'.

bamPath

The column name that identifies where to find the bam file for each subject. Defaults to 'bam_path'.

Value

Returns a data.frame of required sample information for running MDTS.

Examples

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meta <- getMetaData(
'https://raw.githubusercontent.com/JMF47/MDTSData/master/data/pD.ped')

MDTS documentation built on Nov. 1, 2018, 2:24 a.m.