get.sra: get.sra

In palmid: RdRP Analysis Suite

Description

Retrieve the SRA runs containing a 'palm_id'-matching contig.

Usage

get.sra(palm_ids, con, ret_df = FALSE, ret_contig.df = FALSE, qc = TRUE)

Arguments

palm_ids	character or list, set of 'palm_id' to lookup in palmdb
con	pq-connection, use SerratusConnect()
ret_df	boolean, return a 'palm_id' 'run_id', 'coverage', 'qsequence' data.frame [F]
ret_contig.df	boolean, return a data.frame of matching contigs [F]
qc	boolean, require 85-percent palmprint coverage and e-value < 1e-6

Value

character, de-duplicated run_ids with a potential match for 'palm_ids'

Examples

palmid_of_interest <- c("u1337")
con <- SerratusConnect()

palm.sra   <- get.sra(palmid_of_interest, con)

palmid documentation built on Oct. 15, 2021, 9:06 a.m.