Package Documentation

Helpfile for phipmake package.

phipmake

phipmake: PhIP-seq Data Analysis Pipeline.

User Functions

Functions intended to be called by user.

define_plan()

Initialize and return drake_plan object. New for github drake 7.0+.

write_drake_params()

write_drake_params

Annotation Functions

For adding & interacting with metadata.

annotate_data()

Add peptide/protein annotation to data file.

read_annot()

Read annotation file based on md path and library name.

read_annot_list()

Read annotation files based on library names and metadata path.

read_pairs()

Read BLAST pairs file based on md path and library name.

read_pairs_list()

Read blast alignment pair files based on library names and metadata path.

u_pep_id_to_libnames()

Take ids of the form HumanLarma_000_<sequence> and returns unique libraries

Prosum and Promax

For basic collapsing of peptide-level data to protein-level.

compute_prosum()

For multilibrary data, identify libraries, and call library_prosum for each.

library_prosum()

For one peptide library, identify proteins from annotation file, and then call protein_prosum for each protein.

protein_prosum()

Take data frame input and calculate the sum of values in each column or row.

compute_promax()

For multilibrary hits data, identify libraries, and call library_promax for each.

library_promax()

For one peptide library, identify proteins from annotation file, and then call protein_promax for each protein.

protein_promax()

Take data frame input and calculate the maximum value in each column or row.

Hits and Polyclonal

Processing enrichment data based on a threshold.

compute_hits()

For multilibrary enrichment, identify libraries, and identify values above threshold. for each.

compute_polycl()

For multilibrary hits data, identify libraries, and call library_polycl for each.

library_polycl()

For one peptide library, identify proteins from annotation file, and then call protein_polycl for each protein.

protein_polycl()

Take data frame input and calculate the polyclonal score in each column or row.

independence_filter()

Compute independent hits usingg network graphing.

Helper Functions

Small functions for various tasks.

check_order()

Maintains specified order of panlibrary data after a call to dplyr::bind_rows.

getparam()

Function to retreive value of parameter from param name.

pbar()

Wrapper for txtProgressBar with some defualt settings.

split_data()

Separate multilibrary peptide data into a phipmake list.

subset_data()

Pull out specific sublibrary data from a larger data frame based on first column grep.

prepare_blast_pairs()

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()

trim alignment dictionary to not include self alignments or redundant values

write_data()

A wrapper for data.table::fwrite to write file to drive.

gather_samples()

read in multiple input files and extract specified columns

prepare_avarda_names()

swap out u_pep_id names for older pep_id names to improve AVARDA speed