setBatchParam: Set Processing Batch Parameter(s)

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

Set Processing Batch Parameter(s)

Description

Sets parameter(s) associated with the currently loaded processing batch. Based on setDadaOpt.

Usage

setBatchParam(..., verbose = TRUE)

Arguments

...	The processing parameters to set, along with their new value.
verbose	Default TRUE. Whether to print a message confirming the assignment of a parameter.

Details

Quality filtering parameters, used as defaults in filterAndTrim:

MAX_EE_FWD, MAX_EE_REV: max. allowable expected errors in forward/reverse reads that pass filter MIN_LEN_FWD, MIN_LEN_REV: min. allowable length of reads that pass filter in forward/reverse reads TRUNC_Q_FWD, TRUNC_Q_REV: base quality score after which to truncate the sequence in forward/reverse reads TRUNC_LEN_FWD, TRUNC_LEN_REV: length of read after which to truncate the sequence in forward/reverse reads. Reads shorter than this value are discarded.

Parameters for DADA options, including heuristics: see setDadaOpt

Value

No value is returned.

See Also

filterAndTrim, setDadaOpt

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