add_psp: Add psp

In bhagwataditya/autonomics: Unified Statistical Modeling of Omics Data

Add psp

Description

Add PhosphoSitePlus literature counts

Usage

add_psp(
  object,
  pspfile = file.path(R_user_dir("autonomics", "cache"), "phosphositeplus",
    "Phosphorylation_site_dataset.gz")
)

Arguments

object	SummarizedExperiment
pspfile	phosphositeplus file

Details

Go to www.phosphosite.org
Register and Login.
Download Phosphorylation_site_dataset.gz'.
Save into: file.path(R_user_dir('autonomics','cache'),'phosphositeplus')

Value

SummarizedExperiment

Examples

fosfile <- system.file('extdata/billing19.phosphosites.txt',  package = 'autonomics')
profile <- system.file('extdata/billing19.proteingroups.txt', package = 'autonomics')
object <- read_maxquant_phosphosites(fosfile = fosfile, profile = profile)
fdt(object)
object %<>% add_psp()
fdt(object)

bhagwataditya/autonomics documentation built on Dec. 1, 2024, 12:27 a.m.