sample_community: Simulate sampling of a microbial community.

In wilkox/rdrsimulate: Simulate Microbial Communities and their rRNA:rDNA Ratios

Description

sample_community simulates a sequencing-based sampling experiment on a microbial community, with independent sequencing efforts for rDNA genes and rRNA transcripts. community. This allows for the effects of partial sequencing to be evaluated.

Usage

sample_community(community, nDNA = 20000, nRNA = 20000)

Arguments

community	A tibble containing a microbial community. This will usually be the output of generate_community.
nDNA	Number of rDNA gene sequences to simulate (i.e. rDNA read count)
nRNA	Number of rRNA transcript sequences to simulate (i.e. rRNA read count)

Value

A tibble containing the measured rDNA and rRNA abundances drawn from the community. All OTUs in the input community, including those not detected, will be included. The phantom column indicates 'phantom OTUs' that yielded rRNA transcripts but not rDNA gene sequences.

See Also

generate_community

Examples

community <- generate_community(1000)
sample_community(community, nDNA = 500, nRNA = 500)

wilkox/rdrsimulate documentation built on May 13, 2019, 12:40 p.m.