Prosum and Promax
For basic collapsing of peptide-level data to protein-level.
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compute_prosum()
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For multilibrary data, identify libraries, and call library_prosum
for each. |
library_prosum()
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For one peptide library, identify proteins from annotation file, and then
call protein_prosum for each protein. |
protein_prosum()
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Take data frame input and calculate the sum of values in each column or row. |
compute_promax()
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For multilibrary hits data, identify libraries, and call library_promax
for each. |
library_promax()
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For one peptide library, identify proteins from annotation file, and then
call protein_promax for each protein. |
protein_promax()
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Take data frame input and calculate the maximum value in each column or row. |
Helper Functions
Small functions for various tasks.
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check_order()
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Maintains specified order of panlibrary data after a call to dplyr::bind_rows. |
getparam()
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Function to retreive value of parameter from param name. |
pbar()
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Wrapper for txtProgressBar with some defualt settings. |
split_data()
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Separate multilibrary peptide data into a phipmake list. |
subset_data()
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Pull out specific sublibrary data from a larger data frame based on first column grep. |
prepare_blast_pairs()
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Convert BLAST+ alignment table to two outputs. First, a full symmetrical two
column table of aligning peptides. Second, a subset of the first, including
only intra-protein alignments, for which protein identity is specified by
an annotation file. |
trimDictionary()
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trim alignment dictionary to not include self alignments or redundant values |
write_data()
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A wrapper for data.table::fwrite to write file to drive. |
gather_samples()
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read in multiple input files and extract specified columns |
prepare_avarda_names()
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swap out u_pep_id names for older pep_id names to improve AVARDA speed |