translate_to_hg19 {YAPSA} | R Documentation |
translate_to_hg19
: In hg19 naming convention, chromosome names start
with the prefix chr and the gonosomes are called X and
Y. If data analysis is performed e.g. with
BSgenome.Hsapiens.UCSC.hg19
, this
naming convention is needed. The inverse transform is done with
translate_to_1kG
.
translate_to_1kG
: In 1kG, i.e. 1000 genomes naming convention,
chromosome names have no prefix chr and the gonosomes are called
23 for X and 24 for Y. If data analysis is
performed e.g. with hs37d5.fa
, this naming convention is needed. The
inverse transform is done with translate_to_hg19
.
translate_to_hg19(in_dat, in_CHROM.field = "CHROM", in_verbose = FALSE) translate_to_1kG(in_dat, in_CHROM.field = "chr", in_verbose = FALSE)
in_dat |
GRanges object, VRanges object or data frame which carries one column with chromosome information to be reformatted. |
in_CHROM.field |
String indicating which column of |
in_verbose |
Whether verbose or not. |
GRanges object, VRanges object or data frame identical to
in_dat
, but with the names in the chromosome column replaced (if
dealing with data frames) or alternatively the seqlevels replaced (if
dealing with GRanges or VRanges objects).
test_df <- data.frame(CHROM=c(1,2,23,24),POS=c(100,120000000,300000,25000), dummy=c("a","b","c","d")) hg19_df <- translate_to_hg19(test_df, in_CHROM.field = "CHROM") hg19_df test_df <- data.frame(CHROM=c(1,2,23,24),POS=c(100,120000000,300000,25000), dummy=c("a","b","c","d")) hg19_df <- translate_to_hg19(test_df, in_CHROM.field = "CHROM") onekG_df <- translate_to_1kG(hg19_df, in_CHROM.field = "CHROM") onekG_df