Genetic File Information

library(BinaryDosage)

The routines getbdinfo, getvcfinfo, and getgeninfo return a list with information about the data in the files. The list returned by each of these routines a section common to them all and a list additionalinfo that is specific to the file type.

Common section

The common section has the following elements

The list returned has its class value set to “genetic-info”.

The datasize and indices values are only returned if the parameter index is set equal to TRUE

Binary Dosage Additional Information

The additional information returned for binary dosage files contains the following information.

This list has its class value set to “bdose-info”.

VCF File Additional Information

The additional information returned for VCF files contains the following information.

This list has its class value set to “vcf-info”.

The values for quality, filter, info, and format can have a length of 0 if all the values are missing. They will have a length of 1 if all the values are equal. The number of rows in the datacolumns data frame will be equal to the length of the format value.

GEN File Additional Information

The additional information returned for GEN files contains the following information.

\(g\) indicates the number of alternate alleles the subject has.

This list has its class value set to “gen-info”.