get_gene_from_snp: Get the candidate genes in regions based on significant SNPs...
In YTLogos/ttplot: Tao Yan's Plot Toolkit

Description Usage Arguments Value Author(s) Examples

View source: R/get_gene_from_snp.R

This function is developed to get the candidate genes in regions based on significant SNPs of GWAS results.

get_gene_from_snp(gff, sig.snp, distance = 75000, file.save = TRUE,
  file.type = "csv", gff.chrom = NA, snp.chrom = NA, geneid = NA,
  pvalue = NA, gene_start = NA, gene_end = NA, snp_location = NA,
  verbose = TRUE, ...)

`gff`	a data frame of all the gene (transcript), must have column names.
`sig.snp`	a data frame of significant SNPs.
`distance`	numeric (bp), it is to define the region. The default is 50000, you need to choose it based on the LD distance in your study.
`file.save`	a logical, if file.output=TRUE, the result will be saved. if file.output=FALSE, the result will be printed. The default is TRUE.
`file.type`	a character, users can choose the different output formats, so far, "csv", "txt", "xlsx" can be selected by users. The default is "csv".
`gff.chrom`	Name of the column containing the chromosome identifers in the gff file; default is NA.
`snp.chrom`	Name of the column containing the chromosome identifers in the snp.sig file; default is NA.
`geneid`	Name of the column containing the geneid in gff file; default is NA.
`pvalue`	Name of the column containing the p values in snp.sig file; default is NA.
`snp_location`	Name of the column containing the snp position in snp.sig file; default is NA.