add_jervis_bardy: Apply the taxon QC method of Jervis-Bardy

In SWittouck/tidyamplicons: Functions to Manipulate and Visualize Amplicon Abundance Data

Apply the taxon QC method of Jervis-Bardy

Description

Function to estimate spearman correlation between relative abundance and sample dna concentration, for each taxon.

Usage

add_jervis_bardy(ta, dna_conc, sample_condition = T, min_pres = 3)

Arguments

ta	A tidyamplicons object.
dna_conc	A variable in the samples table that contains dna concetrations (unquoted).
sample_condition	An optional extra condition that samples must pass before calculations.
min_pres	The minimum number of samples a taxon has to be present in for its correlation to be calculated.

Details

See: J. Jervis-Bardy et al., “Deriving accurate microbiota profiles from human samples with low bacterial content through post-sequencing processing of Illumina MiSeq data,” Microbiome, vol. 3, no. 1, Art. no. 1, 2015, doi: 10.1186/s40168-015-0083-8.

SWittouck/tidyamplicons documentation built on Aug. 15, 2023, 3:14 a.m.