getMetaData: Constructor for metadata

In MDTS: Detection of de novo deletion in targeted sequencing trios

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

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

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

MDTS documentation built on Nov. 8, 2020, 6:23 p.m.