get.sraSTAT: get.sraSTAT

In ababaian/palmid: Viral RNA Dependent RNA Polymerase Analysis Suite

get.sraSTAT

Description

Retrieve the STAT-taxonomy (at the rank of 'order') and the grouping labels for a set of SRA run_ids

Usage

get.sraSTAT(run_ids, con = SerratusConnect(), prc_threshold = 5)

Arguments

run_ids	character, SRA 'run_id'
con	pq-connection, use SerratusConnect()
prc_threshold	numeric, threshold percent of total reads for tax to retain [5]

Details

Data from NCBI-STAT (Katz et al., 2021)

Value

data.frame, with 'run_id', 'order_name', 'label' columns

Examples

 # Retrieve STAT taxonomic orders for a SRA run
 # and show all results with prc_threshold of 0%
con <- SerratusConnect()
sra.stat   <- get.sraSTAT('ERR2756788', con, prc_threshold = 0)

#NOTE: 'pident' column will be NA, match values from palm.sra object

ababaian/palmid documentation built on July 1, 2023, 1:09 a.m.