AnnotationGenerator: generate case control annotations for hit data based on...

In brandonsie/phipcc: Generate Case-Control Reports from PhIP-seq Data

Description

generate case control annotations for hit data based on library annotation file.

Usage

AnnotationGenerator(data, data_level, data_types, annot,
  peptide_col_id_match, protein_col_id_match, peptide_col_id_display,
  protein_col_id_display, description_col_id, flag_col_id, flag_type,
  pep_aa = "pep_aa")

Arguments

data	Input data frame.
data_level	If data_level is "peptide", then AnnotationGenerator will operate based on the peptide_ parameters. If data_level is "protein", then Annotation_Generator will operate based on the protein_ parameters.
data_types	Character vector describing types of data stored in data list. e.g. "zscore", "polyclonal".
annot	Library annotation file with named columns.
peptide_col_id_match	For data_level=="peptide", the name of a column in annot that corresponds to the first column of data.
protein_col_id_match	For data_level=="protein", the name of a column in annot that corresponds to the first column of data.
protein_col_id_display	The name of a column in annot that corresponds to identifiers to display in the markdown report corresponding to each protein.
description_col_id	The name of a column in annot that corresponds to identifiers to display in the markdown report corresponding to gene product or similar short protein descriptions to display in the markdown report.
flag_col_id	Character string or vector of column name(s) corresponding to annotation flags to indicate in the markdown report (e.g. of known autoantigens or surface proteins).
flag_type	type "binary" to detect whether or not there is text in that cell. "literal" to display exact text from cell.
pep_aa	Character string of column name in annot corresponding to peptide amino acid sequence in the markdown report. Needed for peitopefindr.
peptide_cold_id_display	For data_level=="peptide", the name of a column in annot that corresponds to identifiers to display in the markdown report corresponding to each peptide.

brandonsie/phipcc documentation built on June 2, 2020, 6:19 a.m.