| splitChr | R Documentation |
Split all chromosomes from the sorted chromosome list
splitChr(tex = tex, chr = chr, sex = FALSE, outdir = ".")
tex |
The sorted chromosome list made by sortList function. |
chr |
The chromosome number sequence, if the chromosome list is "single" which means a single character following "chr" in the Fasta identifier, be sure starting with 1 and ending with 9; if the chromosome list is "double" which means two characters following "chr" in the Fasta identifier, be sure that starting with 10 but the ending can be changed. |
sex |
Whether to output the sex chromosomes like X chromosome and Y chromosome. |
outdir |
The output directory. |
Write the splitted chromosome Fasta file to separated txt files according to the chromosome number.
Shaoqian Ma
data(tex) data(text) #Simplify the Fasta id text<- replaceText(type = "text",input = text) #Subtract id id <- subFasID(text = text) #Sort the fasta according to the chromosome number in id tex2<- sortList(id=id,tex = tex,chrsig = "single") tex3 <- sortList(id=id,tex = tex,chrsig = "double") outdir <- tempdir() #Output the results splitChr(tex = tex2,chr=seq(1,9),sex = TRUE,outdir = outdir) splitChr(tex = tex3,chr=seq(10,22),sex = FALSE,outdir = outdir)