Docstring:
Usage: qiime pepsirf bin [OPTIONS]
Creates groups of peptides with similar starting abundances with pepsirf's
bin module
Inputs:
--i-scores ARTIFACT FeatureTable[Normed¹ | NormedDifference |
NormedDiffRatio | NormedRatio | NormedSized²]
Input tab-delimited normalized score matrix file to
use for peptide binning. This matrix should only
contain info for the negative control samples that
should be used to generate bins (see subjoin module
for help generatinig input matrix). Peptides with
similar scores, summed across the negative controls,
will be binned together. [required]
Parameters:
--p-allow-other-normalization VALUE Bool % Choices(False)¹ | Bool %
Choices(True)² [default: False]
--p-bin-size INTEGER The minimum number of peptides that a bin must
Range(1, None) contain. If a bin would be created with fewer than
bin-size peptides, it will be combined with the next
bin until at least bin-size peptides are found.
[default: 300]
--p-round-to INTEGER The 'rounding factor' for the scores parsed from the
Range(0, None) score matrix prior to binning. Scores found in the
matrix will be rounded to the nearest 1/10^x for a
rounding factor x. For example, a rounding factor of 0
will result in rounding to the nearest integer, while
a rounding factor of 1 will result in rounding to the
nearest tenth. [default: 0]
--p-outfile TEXT The outfile that will produce a list of inputs to
PepSIRF. [default: './bin.out']
--p-pepsirf-binary TEXT
The binary to call pepsirf on your system.
[default: 'pepsirf']
Outputs:
--o-bin-output ARTIFACT
PeptideBins¹'² PeptideBins file that contains one bin per line and
each bin will be a tab-delimited list of the names of
the peptides in the bin. [required]
Miscellaneous:
--output-dir PATH Output unspecified results to a directory
--verbose / --quiet Display verbose output to stdout and/or stderr during
execution of this action. Or silence output if
execution is successful (silence is golden).
--example-data PATH Write example data and exit.
--citations Show citations and exit.
--help Show this message and exit.
Import:
from qiime2.plugins.pepsirf.methods import bin
Docstring:
pepsirf bin module
Creates groups of peptides with similar starting abundances with pepsirf's
bin module
Parameters
----------
scores : FeatureTable[Normed¹ | NormedDifference | NormedDiffRatio | NormedRatio | NormedSized²]
Input tab-delimited normalized score matrix file to use for peptide
binning. This matrix should only contain info for the negative control
samples that should be used to generate bins (see subjoin module for
help generatinig input matrix). Peptides with similar scores, summed
across the negative controls, will be binned together.
allow_other_normalization : Bool % Choices(False)¹ | Bool % Choices(True)², optional
bin_size : Int % Range(1, None), optional
The minimum number of peptides that a bin must contain. If a bin would
be created with fewer than bin_size peptides, it will be combined with
the next bin until at least bin_size peptides are found.
round_to : Int % Range(0, None), optional
The 'rounding factor' for the scores parsed from the score matrix prior
to binning. Scores found in the matrix will be rounded to the nearest
1/10^x for a rounding factor x. For example, a rounding factor of 0
will result in rounding to the nearest integer, while a rounding factor
of 1 will result in rounding to the nearest tenth.
outfile : Str, optional
The outfile that will produce a list of inputs to PepSIRF.
pepsirf_binary : Str, optional
The binary to call pepsirf on your system.
Returns
-------
bin_output : PeptideBins¹'²
PeptideBins file that contains one bin per line and each bin will be a
tab-delimited list of the names of the peptides in the bin.
