#' @name import_vcf
#' @title import vcf from file
#' @author Zhangrenl
#' @usage import_vcf(vcf_file = vcf_file, ...)
#' @description import vcf file
#' @examples
#' \dontrun{
#' data("quickHap_test")
#' vcfR::write.vcf(vcf, file = "test.vcf.gz")
#' vcf <- import_vcf(file = "test.vcf.gz")
#' unlink("test.vcf.gz")
#' }
#' @importFrom vcfR read.vcfR
#' @param vcf_file file path of vcf
#' @param ... pass to vcfR::read.vcfR
#' @usage import_vcf(vcf_file = vcf_file, ...)
#' @export
#' @return vcfR object
import_vcf <- function(vcf_file = vcf_file, ...) {
vcf <- vcfR::read.vcfR(vcf_file, ...)
return(vcf)
}
#' @name import_pheno
#' @title imports phenos from file
#' @usage import_pheno(phenoFile, comment.char = "#", ...)
#' @description first col should be Accessions
#' phenos should loacted begin second col,
#' phenoName should at the first row,
#' If "." located in pheno name, the former part of phenoName will be set as y axis name
#' and the latter part will be set as foot of the fig.
#' @examples
#' \dontrun{
#' data("quickHap_test")
#' write.table(pheno, file = "test.pheno.txt", quote = FALSE, sep = "\t")
#' pheno <- import_pheno("test.pheno.txt")
#' unlink("test.pheno.txt")
#'}
#' @importFrom utils read.delim
#' @param phenoFile pheno file path, should be a table separated by tab
#' @param comment.char comment.char, start with comment.char will be ignored
#' @param ... parameters will pass to read.delim
#' @export
#' @return data.frame, Accession names were set as rownames and cols were
#' named by pheno names
import_pheno <- function(phenoFile, comment.char = "#", ...){
phenos <- utils::read.delim(phenoFile,
check.names = FALSE,
row.names = 1,
comment.char = comment.char, ...)
return(phenos)
}
#' @name import_gff
#' @title import_gff
#' @usage import_gff(gffFile, format = "GFF")
#' @examples
#' \dontrun{
#' gff <- import_gff("your.gff", format = "GFF")
#' }
#' @importFrom rtracklayer import
#' @param gffFile gff file path
#' @param format defalt as GFF
#' @export
#' @return GRange object
import_gff <- function(gffFile, format = "GFF"){
rtracklayer::import(gffFile, format = "GFF")
}
#' @name import_hapResult
#' @title import_hapResult
#' @usage import_hapResult(file)
#' @examples
#' \dontrun{
#' hapResult <- import_hapResult("your_hapResult_file.txt")
#' }
#' @importFrom rtracklayer import
#' @param file hapResult file path
#' @export
#' @return data.frame
import_hapResult <- function(file){
hapResult <- read.delim(file, header = F)
colnames(hapResult) <- hapResult[2,]
return(hapResult)
}
`%>%` <- magrittr::`%>%`
`%over%` <- IRanges::`%over%`
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