Python API
The Python API enables maximum flexibility using crema.
Read PSMs easily using the read_tide()
or
read_mztab()
functions for files in the Tide
tab-delimited format or mzTab format, respectively. Alternatively,
more generic tab delimited files can be read using the read_txt()
.
Once read, a collection of PSMs is stored in a PsmDataset
object.
Calling the assign_confidence()
function will calculate confidence estimates
for the respective psm data using the specified confidence estimate method.
This will produce a confidence
object that stores the calculated
confidence estimates via false discovery rates (FDR) and q-values. Results stored in a
confidence
object can be exported by calling the to_txt()
function.
Functions
Primary Functions
Assign confidence estimates to a collection of peptide-spectrum matches. |
Parsers
Read peptide-spectrum matches (PSMs) from Tide tab-delimited files. |
|
Read peptide-spectrum matches (PSMs) from MSAmanda tab-delimited files. |
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Read peptide-spectrum matches (PSMs) from MSFragger pepXML files. |
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Read peptide-spectrum matches (PSMs) from MSGF+ tab-delimited files. |
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Read peptide-spectrum matches (PSMs) from pepXML files. |
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Read peptide-spectrum matches (PSMs) from mzTab files. |
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Read peptide-spectrum matches (PSMs) from delimited text files. |
Writers
Save confidence estimates to delimited text files. |
Dataset
Store a collection of peptide-spectrum matches (PSMs). |
Confidence
|
Estimate statistical confidence estimates for a collection of PSMs. |