README.md

In Przemol/WB.WS259: WormBase genome annotations R package

WormBase genome annotations R package

Installation

if (!require("devtools")) install.packages("devtools")
devtools::install_github('przemol/WB.WS259', build_vignettes=FALSE)

Usage

• Load packageL

library(WB.WS259)

• List data:

data(package = 'WB.WS259')

• Load data:

data(wb.enhancer)
wb.enhancer

• Extract metadata:

data(wb.gene)
elementMetadata(wb.gene)

• Save as BED (UCSC chromosome names, e.g. chrII):

getBED('wb.rRNA')

• Save as BED (WB/Ensembl chromosome names, e.g. II):

getBED('wb.rRNA', chromosomes = 'Ensembl')

Available data

|feature |count |length_bp |genome_pct |memory |metadata_columns | |:--------------------------------------|:-------|:----------|:----------|:--------|:--------------------------------------------------------------------------------------------------| |wb.antisense_RNA |104 |99164 |0.0946 |51.5 Kb |source;type;ID;Name;Parent | |wb.assembly_component |6541 |306303393 |100 |551.7 Kb |source;type;genbank;Name | |wb.base_call_error_correction |1553 |5385 |0.00537 |145.4 Kb |source;type;Name | |wb.binding_site |93185 |2539659 |1.8 |4.5 Mb |source;type;score;Name;tf_id;tf_name | |wb.biological_region |37 |272364964 |90.5 |27.5 Kb |source;type;balancer;balancer_type | |wb.CDS |2720054 |514846890 |36.5 |223.6 Mb |source;type;phase;ID;Name;locus;wormpep;prediction_status | |wb.complex_substitution |50691 |11556816 |4.93 |10.3 Mb |source;type;variation;public_name;polymorphism;consequence;insertion;aachange;engineered | |wb.conserved_region |429231 |186654329 |52.8 |45.8 Mb |source;type;Target | |wb.deletion |148242 |345017343 |56.9 |25.5 Mb |source;type;variation;public_name;polymorphism;consequence;status;insertion;rflp;engineered | |wb.DNAseI_hypersensitive_site |7095 |857295 |0.855 |578.4 Kb |source;type;Name | |wb.duplication |3484 |8112949 |6.47 |296.2 Kb |source;type;Name | |wb.enhancer |2430 |1018498 |1 |214.1 Kb |source;type;Name | |wb.exon |384457 |83175264 |33.6 |15.8 Mb |source;type;Parent | |wb.experimental_result_region |20029 |30358067 |27.5 |1.5 Mb |source;type;Name | |wb.expressed_sequence_match_I |1550464 |160353732 |6.39 |212.9 Mb |source;type;score;ID;Target;species | |wb.expressed_sequence_match_II |1612288 |167409080 |6.4 |220.5 Mb |source;type;score;ID;Target;species | |wb.expressed_sequence_match_III |1358231 |144804782 |5.79 |187.4 Mb |source;type;score;ID;Target;species | |wb.expressed_sequence_match_IV |1775932 |201455076 |6.4 |235.6 Mb |source;type;score;ID;Target;species | |wb.expressed_sequence_match_MtDNA |32240 |6305685 |0.0135 |4.7 Mb |source;type;score;ID;Target;species | |wb.expressed_sequence_match_V |1902470 |189084188 |7.91 |257 Mb |source;type;score;ID;Target;species | |wb.expressed_sequence_match_X |1452995 |138602285 |5.4 |197.2 Mb |source;type;score;ID;Target;species | |wb.five_prime_UTR |30806 |2350538 |1.51 |2.5 Mb |source;type;Parent | |wb.G_quartet |2907 |69118 |0.0538 |259.2 Kb |source;type;Target | |wb.gene |74216 |350167639 |92.4 |19.4 Mb |source;type;ID;Name;gmap;status;interpolated_map_position;sequence_name;biotype;locus | |wb.histone_binding_site |5164 |5330550 |5.32 |427.5 Kb |source;type;Name | |wb.insertion_site |90429 |90429 |0.081 |17 Mb |source;type;variation;public_name;polymorphism;consequence;status;insertion;rflp;engineered | |wb.intron |738238 |1024110369 |87.6 |17.6 Mb |source;type;score | |wb.inverted_repeat |65691 |6067299 |5.86 |2.8 Mb |source;type;score;Note | |wb.lincRNA |178 |216777 |0.209 |79 Kb |source;type;ID;Name;Parent;locus | |wb.low_complexity_region |189148 |5985910 |5.97 |5.1 Mb |source;type;Note | |wb.miRNA_primary_transcript |10 |5716 |0.00333 |29.2 Kb |source;type;ID;Name;Parent | |wb.miRNA |454 |10136 |0.00996 |138.5 Kb |source;type;ID;Name;Parent;locus | |wb.mRNA_region |227070 |2372572 |2.37 |7.8 Mb |source;type;score;Note | |wb.mRNA |33667 |133840722 |62.2 |9.4 Mb |source;type;ID;Name;Parent;locus;wormpep | |wb.nc_primary_transcript |833 |2608515 |2.11 |157.6 Kb |source;type;ID;Name | |wb.ncRNA |11399 |1646133 |1.39 |1.7 Mb |source;type;score;ID;Name;locus | |wb.nucleotide_match |25489 |442391182 |83.5 |2.7 Mb |source;type;score;ID;Target;Name | |wb.operon |1498 |15210583 |14.5 |383.2 Kb |source;type;Name;genes | |wb.PCR_product |83377 |125766915 |62.4 |8.6 Mb |source;type;Name;amplified;vendorID | |wb.piRNA |15364 |322644 |0.255 |4.6 Mb |source;type;ID;Name;Parent;locus | |wb.point_mutation |1076128 |1076128 |0.858 |160.2 Mb |source;type;variation;public_name;consequence;substitution;aachange;engineered | |wb.polyA_signal_sequence |2454 |14724 |0.0145 |224.5 Kb |source;type;Name | |wb.polyA_site |87271 |87271 |0.0866 |6.8 Mb |source;type;Name | |wb.polypeptide_motif |383773 |52526148 |19 |40.5 Mb |source;type;ID;cds;predictiontype;range;exons;protein | |wb.possible_base_call_error |1233 |6619 |0.00659 |120.4 Kb |source;type;Name | |wb.pre_miRNA |257 |22154 |0.0218 |103.3 Kb |source;type;ID;Name;Parent;locus | |wb.promoter |95 |92870 |0.0909 |31.8 Kb |source;type;Name | |wb.protein_coding_primary_transcript |15594 |54820681 |34 |2.4 Mb |source;type;ID;Name | |wb.protein_match |3022263 |616204488 |56.3 |299.5 Mb |source;type;score;Target | |wb.pseudogenic_rRNA |1 |852 |0.00085 |27 Kb |source;type;ID;Name;Parent | |wb.pseudogenic_transcript |2031 |3377939 |2.97 |384.4 Kb |source;type;ID;Name;locus | |wb.pseudogenic_tRNA |209 |15216 |0.0152 |77.4 Kb |source;type;ID;Name;Parent | |wb.reagent |519568 |54087025 |30.1 |52.6 Mb |source;type;Target;Name | |wb.regulatory_region |73 |2773 |0.00266 |31.5 Kb |source;type;Name;tf_id;tf_name | |wb.repeat_region |116933 |18197219 |16.2 |9.3 Mb |source;type;score;Target | |wb.RNAi_reagent |342818 |188679730 |48.3 |38.5 Mb |source;type;Target;laboratory;history_name | |wb.rRNA |22 |10674 |0.0106 |33.4 Kb |source;type;ID;Name;Parent;locus | |wb.SAGE_tag |292984 |4788083 |3.72 |23.7 Mb |source;type;sequence;count;gene;transcript | |wb.scRNA |1 |105 |0.000105 |27.1 Kb |source;type;ID;Name;Parent;locus | |wb.SL1_acceptor_site |43207 |86414 |0.0861 |3.4 Mb |source;type;Name | |wb.SL2_acceptor_site |13445 |26890 |0.0268 |1.1 Mb |source;type;Name | |wb.snoRNA |345 |47330 |0.0472 |112.6 Kb |source;type;ID;Name;Parent;locus | |wb.SNP |728906 |728906 |0.657 |126.3 Mb |source;type;variation;public_name;polymorphism;consequence;status;substitution;aachange;rflp | |wb.snRNA |130 |15978 |0.0156 |61.2 Kb |source;type;ID;Name;Parent;locus | |wb.substitution |10036 |40319 |0.017 |1.4 Mb |source;type;variation;public_name;polymorphism;consequence;status;substitution;aachange;engineered | |wb.tandem_duplication |4024 |445639486 |98.9 |705.3 Kb |source;type;variation;public_name;polymorphism;consequence;insertion | |wb.tandem_repeat |53024 |6793271 |4.78 |2 Mb |source;type;score;Note | |wb.TF_binding_site |885742 |406860440 |41.1 |51.4 Mb |source;type;Name;tf_id;tf_name | |wb.three_prime_UTR |49281 |9700647 |3.22 |2.4 Mb |source;type;Name | |wb.transcribed_fragment |4095280 |874039535 |50.3 |140.6 Mb |source;type;score;Note | |wb.transcript_region |2024683 |71492795 |39.7 |76.5 Mb |source;type;score;Note | |wb.transcription_end_site |92672 |92672 |0.0708 |7.1 Mb |source;type;Name | |wb.translated_nucleotide_match |143840 |6152928 |4.13 |18.5 Mb |source;type;Target;protein_matches;cds_matches;times_observed | |wb.transposable_element_insertion_site |15904 |15904 |0.0136 |2.6 Mb |source;type;variation;public_name;polymorphism;consequence;insertion | |wb.transposable_element |11256 |4543722 |4.37 |2.1 Mb |source;type;ID;Name;Family | |wb.tRNA |634 |47053 |0.0469 |185.7 Kb |source;type;ID;Name;Parent;locus | |wb.TSS_region |73499 |2626912 |2.54 |5.9 Mb |source;type;Name |

Przemol/WB.WS259 documentation built on May 12, 2019, 1:59 p.m.