The *_LTRpred_DataSheet.tsv file generated by LTRpred stores the features of all predicted LTR transposons in a table. This function
imports this LTRpred output table.
read.ltrpred(data.sheet)
| data.sheet | path to the |
|---|
Hajk-Georg Drost
# example prediction file generated by LTRpred pred.file <- system.file("Hsapiens_ChrY_LTRpred_DataSheet.tsv", package = "LTRpred") # read LTRpred generated prediction file (data sheet) pred <- read.ltrpred(pred.file) # or arrange by ltr_similarity dplyr::arrange(tidy.datasheet(pred), dplyr::desc(ltr_similarity)) #> # A tibble: 21 × 73 #> ID chromosome start end strand dfam_target_name dfam_acc width #> <chr> <chr> <int> <int> <chr> <chr> <chr> <int> #> 1 Hsapiens_Ch… NC000024.1… 4.36e6 4.36e6 - NA NA 5840 #> 2 Hsapiens_Ch… NC000024.1… 5.32e6 5.33e6 - NA NA 5644 #> 3 Hsapiens_Ch… NC000024.1… 3.28e6 3.30e6 - NA NA 24131 #> 4 Hsapiens_Ch… NC000024.1… 4.33e6 4.33e6 + NA NA 6498 #> 5 Hsapiens_Ch… NC000024.1… 3.45e6 3.47e6 + NA NA 17561 #> 6 Hsapiens_Ch… NC000024.1… 3.39e6 3.41e6 - NA NA 20864 #> 7 Hsapiens_Ch… NC000024.1… 3.74e6 3.76e6 - NA NA 16196 #> 8 Hsapiens_Ch… NC000024.1… 3.37e6 3.39e6 + NA NA 12952 #> 9 Hsapiens_Ch… NC000024.1… 4.42e6 4.42e6 + NA NA 5724 #> 10 Hsapiens_Ch… NC000024.1… 3.72e6 3.73e6 - NA NA 11171 #> # … with 11 more rows, and 65 more variables: ltr_similarity <dbl>, orfs <int>, #> # protein_domain <chr>, Clust_Cluster <chr>, Clust_Target <chr>, #> # Clust_Perc_Ident <dbl>, Clust_cn <int>, cn_3ltr <dbl>, cn_5ltr <dbl>, #> # lLTR_start <int>, lLTR_end <int>, lLTR_length <int>, rLTR_start <int>, #> # rLTR_end <int>, rLTR_length <int>, lTSD_start <int>, lTSD_end <int>, #> # lTSD_motif <chr>, rTSD_start <int>, rTSD_end <int>, rTSD_motif <chr>, #> # PPT_start <int>, PPT_end <int>, PPT_motif <chr>, PPT_strand <chr>, …