get.sOTU: get.sOTU

In palmid: RdRP Analysis Suite

Description

Retrieve the parent sOTU for a 'palm_id' in palmdb or the set of all children 'palm_id' within an species/sOTU

Usage

get.sOTU(palm_ids, con, get_childs = FALSE, ordinal = FALSE)

Arguments

palm_ids	character, set of 'palm_id' to lookup in palmdb
con	pq-connection, use SerratusConnect()
get_childs	boolean, return all children 'palm_id' instead of parent sOTU [FALSE]
ordinal	boolean, return an ordered sOTU vector based on input 'palm_ids'

Value

character, unique 'palm_id' sOTU or sOTU-children

Examples

## R Code Example
 
con <- SerratusConnect()
get.sOTU(c("u1337"), con, get_childs = TRUE)


## Non-Running Example to demonstrate sOTU Relationships
# palm_id    sOTU
# u1         u3
# u2         u3
# u3         u3
# u4         u4

# Retrieve the parent sOTU for an input of palm_ids
# get.sOTU(c("u1","u2",u4"), con, get_childs = FALSE)
# -- returns c("u3","u4")

# Return an ordinal list of sOTU for iput
# get.sOTU(c("u2","u4","u2","u1"), con, ordinal = TRUE)
# -- returns c("u3", "u4", "u3", "u3")

# Return all children palm_id within an sOTU
# get.sOTU(c("u2"), con, get_childs = TRUE)
# -- returns c("u1", u2", "u3")

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