sids_get: Return random set of sequence IDs

Description Usage Arguments Details Value See Also

View source: R/tools-entrez.R


For a given txid return a random set of sequences associated.


sids_get(txid, direct, ps, retmax = 100, hrdmx = 1e+05)



NCBI taxon identifier


Node-level only or subtree as well? Default FALSE.


Parameters list, generated with parameters()


Maximum number of sequences when querying model organisms. The smaller the more random, the larger the faster.


Absolute maximum number of sequence IDs to download in a single query.


For model organisms downloading all IDs can a take long time or even cause an xml parsing error. For any search with more than hrdmx sequences, this function we will run multiple small searches downloading retmax seq IDs at a time with different retstart values to generate a semi-random vector of sequence IDs. For all other searches, all IDs will be retrieved. Note, it makes no sense for mdlthrs in parameters to be greater than hrdmx in this function.


vector of IDs

See Also

Other run-private: batcher, blast_clstr, blast_filter, blast_setup, blast_sqs, blastcache_load, blastcache_save, blastdb_gen, blastn_run, cache_rm, cache_setup, clade_select, clstr2_calc, clstr_all, clstr_direct, clstr_sqs, clstr_subtree, clstrarc_gen, clstrarc_join, clstrrec_gen, clstrs_calc, clstrs_join, clstrs_merge, clstrs_renumber, clstrs_save, cmdln, descendants_get, download_obj_check, error, gb_extract, hierarchic_download, info, ncbicache_load, ncbicache_save, obj_check, obj_load, obj_save, outfmt_get, parameters_load, parameters_setup, parent_get, progress_init, progress_read, progress_reset, progress_save, rank_get, rawseqrec_breakdown, safely_connect, search_and_cache, searchterm_gen, seeds_blast, seq_download, seqarc_gen, seqrec_augment, seqrec_convert, seqrec_gen, seqrec_get, sids_check, sids_load, sids_save, sqs_count, sqs_save, stage_args_check, stages_run, tax_download, taxdict_gen, taxtree_gen, txids_get, txnds_count, warn

ropensci/phylotaR documentation built on Jan. 16, 2020, 11:47 a.m.