read_netphorest: Read in NetPhorest prediction output

In casblaauw/phosphocie: Create Continuous Phosphosite Colour Representations

Read in NetPhorest prediction output

Description

Read in NetPhorest input. Keeps only kinase scores.

Usage

read_netphorest(
  path,
  return_long = FALSE,
  cols_to_keep = c("fasta_id", "position", "residue", "fragment_11")
)

Arguments

path	Path to the netphorest output file
return_long	Optional boolean: whether to return the data in long format (kinases on rows, like raw data), or whether to widen data (kinases as columns, for use with U-CIE). Default is false (return wide)
cols_to_keep	Columns to keep when pivoting to wide data. By default, keeps 'fasta_id', 'position', 'residue', and 'fragment_11', and drops 'method', 'organism', and 'binder_type'.

Value

A tibble with site/protein data and kinase scores

Examples

kinsub_netphorest_path <- system.file('extdata', 'kinsub_human_netphorest', package = 'phosphocie')
kinsub_netphorest <- read_netphorest(kinsub_netphorest_path)

casblaauw/phosphocie documentation built on March 30, 2022, 8:28 p.m.