load_edge_assignment: Efficiently loads an EDGE-produced taxonomic assignment from...

In LANL-Bioinformatics/MetaComp: EDGE Taxonomy Assignments Visualization

Description

Efficiently loads an EDGE-produced taxonomic assignment from a file. An assumption has been made – since EDGE tables are generated in an automated fashion, they should be properly formatted – thus the code doesn't check for any inconsistencies except for the very file existence. Note however, the unassigned to taxa entries are removed. This implementation fully relies on the fread function from data.table package gaining performance over traditional R techniques.

Usage

load_edge_assignment(filepath, type)

Arguments

filepath	the path to EDGE-generated tab-delimited taxonomy assignment file.
type	the assignment type. Following types are recognized: 'bwa', 'diamond', 'gottcha', 'gottcha2', 'kraken', 'metaphlan', and 'pangia'.

Value

a data frame containing four columns: TAXA, LEVEL, COUNT, and ABUNDANCE, representing taxonomically anchored sequences from the sample.

Examples

pa_fpath <- system.file("extdata", "HMP_even//allReads-pangia.list.txt", package="MetaComp")
pangia_assignment = load_edge_assignment(pa_fpath, type = "pangia")

table(pangia_assignment$LEVEL)

pangia_assignment[pangia_assignment$LEVEL == "phylum",]

LANL-Bioinformatics/MetaComp documentation built on May 8, 2019, 4:51 p.m.