collapseNoMismatch2: Combine together sequences that are identical up to shifts...

In claraqin/neonMicrobe: Downloading, Pre-processing, and Assembling NEON Soil Microbe Marker Gene Sequence Data

Combine together sequences that are identical up to shifts and/or length (with progress bar)

Description

This function adds a simply adds a progress bar to collapseNoMismatch.

Usage

collapseNoMismatch2(
  seqtab,
  minOverlap = 20,
  orderBy = "abundance",
  identicalOnly = FALSE,
  vec = TRUE,
  verbose = FALSE
)

Arguments

seqtab	(Required). A sample by sequence matrix, the return of makeSequenceTable.
minOverlap	(Optional). numeric(1). Default 20. The minimum amount of overlap between sequences required to collapse them together.
orderBy	(Optional). character(1). Default "abundance". Specifies how the sequences (columns) of the returned table should be ordered (decreasing). Valid values: "abundance", "nsamples", NULL.
identicalOnly	(Optional). logical(1). Default FALSE. If TRUE, only identical sequences (i.e. duplicates) are collapsed together.
vec	(Optional). logical(1). Default TRUE. Use the vectorized aligner. Should be turned off if sequences exceed 2kb in length.
verbose	(Optional). logical(1). Default FALSE. If TRUE, a summary of the function results are printed to standard output.

See Also

collapseNoMismatch

claraqin/neonMicrobe documentation built on April 11, 2024, 11:47 a.m.