fetchSequence: Retrieve Sequence from Phyloseq

In RIVM-IIV-Microbiome/biomeUtils: Utilities for microbiome analytics

Retrieve Sequence from Phyloseq

Description

Retrieve Sequence from Phyloseq

Usage

fetchSequence(x, seq_id = NULL, as_DNAStringSet = TRUE)

Arguments

x	A phyloseq object
seq_id	A list of IDs matching taxa_names(phyloseq) that also have sequence information stored in refseq slot of phyloseq object.
as_DNAStringSet	Logical (Default=TRUE). If FALSE sequences are returned as character strings.

Details

Retrieve sequences from refseq slot in phyloseq phyloseq object.

Value

Sequences for user species IDs either as vector or DNAStringSet object

Author(s)

Sudarshan A. Shetty

Examples

library(biomeUtils)
data("SprockettTHData")
ps <- SprockettTHData
seq_id <- c("ASV_30_Lachnospiraceae", "ASV_451_UC5-1-2E3", "ASV_586_CAG-56")
myseqs <- fetchSequence(ps, seq_id = seq_id, as_DNAStringSet = TRUE)
myseqs

RIVM-IIV-Microbiome/biomeUtils documentation built on July 20, 2023, 10:29 a.m.