read_metadt: Read sample file with minimal metadata

In SinomeM/CNVgears: A Framework to Combine, Analize and Interpret CNVs Calling Results

Description

read_medaDT handles the input of the sample table (sampleID, sex, role, famID) in a standardized format.

Usage

read_metadt(
  DT_path,
  sample_ID_col = "sample_ID",
  sex_col = "sex",
  role_col = "role",
  fam_ID_col = "fam_ID"
)

Arguments

DT_path	path to the input file.
sample_ID_col	name of the columns containing the sample ID in the original file;
sex_col	name of the columns containing the sex information in the original file;
role_col	name of the columns containing the role information ID in the original file;
fam_ID_col	name of the columns containing the family ID in the original file;

Details

This function is needed in the first step of virtually every analysis. The input data must have at least the following columns:

• sample ID, self describing;

• sex, ideally in 1/2 format, for males and females, however also "male"/"female" or "Male"/"Female" are accepted;

• role, role of the sample in the family, either "father", "mother", "proband" or "sibling";

• family ID, self describing.

Actual name and order of the columns in the file is not relevant since they are passed to the function via parameter. Since the function in this package are optimized for family based studies, family ID and role information for each sample are required, however if the user is interested only, as an example, in CNVRs computation, genic content annotation or identification of calls in IG regions and does not have such information "role" and famID can be "NA". Note that doing so some functions won't be usable.

Value

cohort metatadata object, a data.table. Will be of the SampleList class in future versions.

Examples

DT <- read_metadt(DT_path = system.file("extdata", "cohort.ped", package = "CNVgears"),
sample_ID_col = "Individual ID", fam_ID_col = "Family ID", sex_col = "Gender",
role_col = "Role")

SinomeM/CNVgears documentation built on Nov. 21, 2021, 5:34 a.m.