Check.entropy.nseq: Check for a subset of FASTA sequences provided as a list,...

In aramette/otu2ot: Calculate oligotypes for aligned FASTA sequences

Description

The function takes one element of a list consisting of sequences (typically belonging to the split in one oligotype), and tests whether the minimum number of sequences and minimum entropy for the subalignment are met.

Usage

Check.entropy.nseq(list.elt, minseq = 0, entropy.min = 0.6)

Arguments

list.elt	one element of a list consisting of sequences (typically belonging to the split in one oligotype. e.g. OT.list.seq[[i]]
minseq	the minimum number of sequences for this subalignment.
entropy.min	the minimum entropy threshold for this subalignment.

Value

The function returns a logical (TRUE/FALSE) whether both conditions are met.

Author(s)

A. Ramette

Examples

#data(mock_env_aligned.list)
#Check.entropy.nseq(mock_env_aligned.list[[2]],minseq=21,entropy.min=0.6) # TRUE
#Check.entropy.nseq(mock_env_aligned.list[[2]],minseq=21,entropy.min=2) # FALSE
#nrow(mock_env_aligned.list[[2]]) # 2500
#Check.entropy.nseq(mock_env_aligned.list[[2]],minseq=2501,entropy.min=0.6) # FALSE

aramette/otu2ot documentation built on May 10, 2019, 12:46 p.m.