Genetic File Information

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

filename - Character value with the complete path and file name of the file with the genetic data
usesfid - Logical value indicating if the subject data has family IDs.
samples - Data frame containing the following information about the subjects
- fid - Character value with family IDs
- sid - Character value with the individual IDs
onchr - Logical value indicating if all the SNPs are on the same chromosome
snpidformat - Integer indicating the format of the SNP IDs as follows
- 0 - Unknown for VCF and GEN files or user specified for binary dosage files
- 1 - chromosome:location
- 2 - chromosome:location:referenceallele:alternateallele
- 3 - chromosome:location_referenceallele_alternateallele
snps - Data frame containing the following values
- chromosome - Character value indicating what chromosome the SNP is on
- location - Integer value with the location of the SNP on the chromosome
- snpid - Character value with the ID of the SNP
- reference - Character value of the reference allele
- alternate - Character value of the alternate allele
snpinfo - List that contain the following information
- aaf - numeric vector with the alternate allele frequencies
- maf - numeric vector with the minor allele frequencies
- avgcall - Numeric vector with the imputation average call
- rsq - Numeric vector with the imputation r squared value
datasize - Numeric vector indicating the size of data in the file for each SNP
indices - Numeric vector indicating the starting location in the file for each SNP

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.

format - numeric value with the format of the binary dosage file
subformat - numeric value with the subformat of the binary dosage file
headersize - integer value with the size of the header in the binary dosage file
numgroups - integer value of the number of groups of subjects in the binary dosage file. This is usually the number of binary dosage files merged together to form the file
groups - integer vector with size of each of the groups

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.

gzipped - Logical value indicating if the file has been compressed using gzip
headerlines - Integer value indicating the number of lines in the header
headersize - Numeric value indicating the size of the header in bytes
quality - Character vector containing the values in QUALITY column
filter - Character vector containing the values in the FILTER column
info - Character vector containing the values in the INFO column
format - Character vector containing the values in the FORMAT column
datacolumns - Data frame summarizing the entries in the FORMAT value containing the following information
- numcolumns - Integer value indicating the number of values in the FORMAT value
- dosage - Integer value indicating the column containing the dosage value
- genotypeprob - Integer value indicating the column containing the genotype probabilities
- genotype - Integer value indicating the column containing the genotype call

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.

gzipped - Logical value indicating if the GEN file is compressed using gz
headersize - Integer value indicating the size of the header in bytes
format - Integer value indicating the number of genotype probabilities for each subject with the following meanings
- 1 - Dosage only
- 2 - \(\Pr(g=0)\) and \(\Pr(g=1)\)
- 3 - \(\Pr(g=0)\), \(\Pr(g=1)\), and \(\Pr(g=2)\)
startcolumn - Integer value indicating in which column the genetic data starts
sep - Character value indicating what value separates the columns

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

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