Import the output file generated with dfam.query.
read.dfam(dfam.file)
| dfam.file | path to Dfam output file generated with |
|---|
Hajk-Georg Drost
# import example Dfam output dfam.file <- read.dfam(system.file("example_dfam.out", package = "LTRpred")) head(dfam.file) #> target_name acc query_name bits #> 1 Copia1-I_DM DF0001559.0 1_CHROMOSOME_dumped__10696719_10701589 57.8 #> 2 Copia_I DF0001563.0 1_CHROMOSOME_dumped__10696719_10701589 154.8 #> 3 Copia1-I_DM DF0001559.0 1_CHROMOSOME_dumped__11148084_11152830 74.8 #> 4 Copia_I DF0001563.0 1_CHROMOSOME_dumped__11148084_11152830 141.9 #> 5 HelitronY4_CE DF0001412.0 1_CHROMOSOME_dumped__11284903_11295619 49.7 #> 6 Copia1-I_DM DF0001559.0 1_CHROMOSOME_dumped__11789447_11794074 218.6 #> e_value bias hmm-st hmm-en strand ali-st ali-en env-st env-en modlen #> 1 1.6e-16 24.2 1329 2113 + 1982 2748 1957 2782 4124 #> 2 7.5e-46 35.2 2862 4321 + 3160 4619 3139 4639 4593 #> 3 1.1e-21 16.1 1326 2030 + 1689 2381 1669 2417 4124 #> 4 5.9e-42 20.3 2858 4355 + 2929 4412 2908 4419 4593 #> 5 2.7e-13 35.6 350 705 + 2131 2483 2122 2503 1855 #> 6 5.3e-65 33.8 1329 2185 + 1621 2483 1594 2503 4124 #> target_description #> 1 LTR retrotransposon from fruit fly: internal portion. #> 2 Drosophila melanogaster transposable element copia. #> 3 LTR retrotransposon from fruit fly: internal portion. #> 4 Drosophila melanogaster transposable element copia. #> 5 HELITRONY4_CE is a family of non-autonomous Helitron DNA transposons #> 6 LTR retrotransposon from fruit fly: internal portion.