Docstring:
Usage: qiime pepsirf zscore [OPTIONS]
Calculate Z scores for each peptide in each sample with pepsirf's zscore
module
Inputs:
--i-scores ARTIFACT FeatureTable[Normed | RawCounts | NormedDifference |
NormedDiffRatio] Name of the file to use as input. Should be a score
matrix in the format as output by the demux and subjoin
modules. Raw or normalized read counts can be used.
[required]
--i-bins ARTIFACT Name of the file containing bins, one bin per line, as
PeptideBins output by the bin module. Each bin contains a
tab-delimited list of peptide names. [required]
Parameters:
--p-trim NUMBER Percentile of lowest and highest counts within a bin
Range(0.0, 100.0) to ignore when calculating the mean and standard
deviation. [default: 2.5]
--p-hdi NUMBER Alternative approach for discarding outliers prior to
Range(0.0, None) calculating mean and stdev. If provided, this argument
will override --trim, which trims evenly from both
sides of the distribution. For --hdi, the user should
provide the high density interval to be used for
calculation of mean and stdev. For example, '--hdi
0.95' would instruct the program to utilize the 95%
highest density interval (from each bin) for these
calculations. [default: 0.0]
--p-num-threads INTEGER
Range(1, None) The number of threads to use for analyses. [default: 2]
--p-outfile TEXT The outfile that will produce a list of inputs to
PepSIRF. [default: './zscore.out']
--p-pepsirf-binary TEXT
The binary to call pepsirf on your system.
[default: 'pepsirf']
Outputs:
--o-zscore-output ARTIFACT FeatureTable[Zscore]
Name for the output Z scores file. This file will be a
FeatureTable[Zscore] with the same dimensions as the
input score file. Each peptide will be written with its
z-score within each sample. [required]
--o-nan-report ARTIFACT
ZscoreNan Name of the file to write out information regarding
peptides that are given a zscore of 'nan'. This occurs
when the mean score of a bin and the score of the focal
peptide are both zero. This will be a ZscoreNan file,
with three columns per line. The first column will
contain the name of the peptide, the second will be the
name of the sample, and the third will be the bin
number of the probe. This bin number corresponds to the
line number in the bins file, within which the probe
was found. [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 zscore
Docstring:
pepsirf zscore module
Calculate Z scores for each peptide in each sample with pepsirf's zscore
module
Parameters
----------
scores : FeatureTable[Normed | RawCounts | NormedDifference | NormedDiffRatio]
Name of the file to use as input. Should be a score matrix in the
format as output by the demux and subjoin modules. Raw or normalized
read counts can be used.
bins : PeptideBins
Name of the file containing bins, one bin per line, as output by the
bin module. Each bin contains a tab-delimited list of peptide names.
trim : Float % Range(0.0, 100.0), optional
Percentile of lowest and highest counts within a bin to ignore when
calculating the mean and standard deviation.
hdi : Float % Range(0.0, None), optional
Alternative approach for discarding outliers prior to calculating mean
and stdev. If provided, this argument will override --trim, which trims
evenly from both sides of the distribution. For --hdi, the user should
provide the high density interval to be used for calculation of mean
and stdev. For example, '--hdi 0.95' would instruct the program to
utilize the 95% highest density interval (from each bin) for these
calculations.
num_threads : Int % Range(1, None), optional
The number of threads to use for analyses.
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
-------
zscore_output : FeatureTable[Zscore]
Name for the output Z scores file. This file will be a
FeatureTable[Zscore] with the same dimensions as the input score file.
Each peptide will be written with its z-score within each sample.
nan_report : ZscoreNan
Name of the file to write out information regarding peptides that are
given a zscore of 'nan'. This occurs when the mean score of a bin and
the score of the focal peptide are both zero. This will be a ZscoreNan
file, with three columns per line. The first column will contain the
name of the peptide, the second will be the name of the sample, and the
third will be the bin number of the probe. This bin number corresponds
to the line number in the bins file, within which the probe was found.
