doc/get_snpdata.md

In FellouMada/rSNPdata: R package for Analysis of P. falciparum whole genome SNPs data

NAME

get_snpdata

USAGE

get_snpdata(vcf.file="file.vcf.gz", meta.file="file.txt", output.dir="/path/to/output/dir", gaf=NULL, gff=NULL)

DESCRIPTION

get_snpdata is a function that create the SNPdata object required for this package.

OPTIONS

vcf.file: the input vcf file (required)
meta.file: the metadata file (required)
output.dir: the path to the folder where the output files will be stored (optional)
gaf: the gene ontology annotation file (optional). this could be downloaded from the PlasmoDB website
gff: the gene annotation file (optional). this could be downloaded from the PlasmoDB website

# RETURN
a SNPdata object with the following elements:

 1.  meta: the metadata table
 2.  details: the genomic coordinates of the SNPs
 3.  GT: the matrix of genotypes
 4.  vcf: the vcf file from which the object was generated
 5.  index: an integer

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FellouMada/rSNPdata documentation built on June 12, 2022, 7:29 p.m.