translate_to_hg19 {YAPSA} | R Documentation

## Translate chromosome names to the hg19 naming convention

### Description

`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`.

### Usage

    translate_to_hg19(in_dat, in_CHROM.field = "CHROM", in_verbose = FALSE)

    translate_to_1kG(in_dat, in_CHROM.field = "chr", in_verbose = FALSE)

### Arguments

`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_dat` carries the chromosome information
`in_verbose` | Whether verbose or not.

### Value

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).

### Examples

    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

[Package YAPSA version 1.20.1 Index]