LiftOver junction IDs using the liftOver tool

Source: R/liftover_junc_id.R

This can be used to liftOver junctions to personalized genome coordinates.

liftover_junc_id(junc_df, chain_file)

Arguments

junc_df

a data.frame with at least one column junc_id containing junction IDs

chain_file

path to a chain file for the UCSC liftOver tool. See also liftOver

Value

a data.frame like the input junc_df with the following additional columns:

  • liftover_successful a logical vector indicating if the liftOver was successful and lifted junction positions build valid genomic intervals and not single positions.

  • liftover_unique a logical vector indicating if the liftOver was unique (1-to-1 correspondence).

  • junc_id_lifted_collapsed a character vector with the lifted junction IDs. Multiple IDs are separated by |. NA represent junc_ids that could not be lifted.

  • junc_id_lifted a character vector with a unique lifted junction IDs. Potentially multiple lifted IDs are combined by the minimal start and maximal end coordinate. NA represent junc_ids that could not be lifted.

Examples


chain_file = system.file(package="liftOver", "extdata", "hg38ToHg19.over.chain")
junc_df <- toy_junc_df
liftover_junc_id(junc_df, chain_file)
#> # A tibble: 17 × 6
#>    junc_id      tx_id liftover_successful liftover_unique junc_id_lifted_colla…¹
#>    <chr>        <chr> <lgl>               <lgl>           <chr>                 
#>  1 chr2:152389… ENST… TRUE                TRUE            chr2:153246510-153248…
#>  2 chr2:152389… ENST… TRUE                TRUE            chr2:153246510-153247…
#>  3 chr2:152389… ENST… TRUE                TRUE            chr2:153246469-153246…
#>  4 chr2:152388… ENST… TRUE                TRUE            chr2:153244924-153248…
#>  5 chr2:152388… ENST… TRUE                TRUE            chr2:153244924-153247…
#>  6 chr2:179415… ENST… TRUE                TRUE            chr2:180280708-180281…
#>  7 chr2:179415… ENST… TRUE                TRUE            chr2:180280714-180280…
#>  8 chr2:179415… ENST… TRUE                TRUE            chr2:180279727-180281…
#>  9 chr2:179445… ENST… TRUE                TRUE            chr2:180310063-180310…
#> 10 chr2:179446… ENST… TRUE                TRUE            chr2:180310952-180310…
#> 11 chr2:179445… ENST… TRUE                TRUE            chr2:180310063-180311…
#> 12 chr2:179642… ENST… TRUE                TRUE            chr2:180506771-180506…
#> 13 chr2:179642… ENST… TRUE                TRUE            chr2:180506873-180506…
#> 14 chr2:179642… ENST… TRUE                TRUE            chr2:180506771-180507…
#> 15 chr2:152226… ENST… TRUE                TRUE            chr2:153083047-153083…
#> 16 chr2:152222… ENST… TRUE                TRUE            chr2:153079245-153079…
#> 17 chr2:152388… ENST… TRUE                TRUE            chr2:153244924-153244…
#> # ℹ abbreviated name: ¹​junc_id_lifted_collapsed
#> # ℹ 1 more variable: junc_id_lifted <chr>