Description Usage Arguments Details Value Examples
View source: R/preprocess_pqpq_data.R
This function is used to prepare Protein Pilot data for analysis in PQPQ.
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df |
A data frame (see details) |
data_type |
one of 'Protein Pilot', 'Spectrum Mill', or 'Proteome Discoverer', depending on the file origin. |
protein_subset |
identifiers for the proteins to be analyzed. |
separate_multiple_protein_IDs |
If true, peptides assigned to multiple proteins are duplicated for each protein to which they are assigned. Otherwise, they are analyzed as a group. |
sample_names |
A character vector identifying the columns holding sample data. |
manually_annotated_fields |
A list containing annotation data. |
Note: this is only tested on the test output from Protein Pilot provided by Jenny Forshed in the PQPQ package, and entered into R using the link{openxlsx}
package. The formatting of data from other
A list, containing the cleaned data.frame and the list of labeled variable names.
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