getFC: Read FlyCodes (FCs)

In cpanse/NestLink: NestLink an R data package to guide through Engineered Peptide Barcodes for In-Depth Analyzes of Binding Protein Ensembles

Read FlyCodes (FCs)

Description

A wrapper function for reading the flycodes using ExperimentHub. The files are used for demonstrating the detectability of the AA sequences. The wrapper functions are extended by columns ssrc prediction and the parentIonMass. The column ESP_Prediction was generated by using the service from https://genepattern.broadinstitute.org.

Usage

getFC(pattern = "^GS[ASTNQDEFVLYWGP]{7}(WR|WLTVR|WQEGGR|WLR|WQSR)$",
  filename = NULL)

Arguments

pattern	a regular expression FlyCode pattern
filename	a two column tab separated file containing a peptide sequence and an ESP value. default is NULL which reads the data provided by the package through ExperimentHub.

Value

a data.frame object of Flycodes

Author(s)

Christian Panse <[e-mail]> 2015, 2018

Source

• https://fgcz-gstore.uzh.ch/projects/p1644/analysis_20170609_o3040/p1644o3482-4_S4.extendedFrags_uniqNB2FC.txt

• https://fgcz-gstore.uzh.ch/projects/p1644/analysis_20170609_o3040/p1644o3482-5_S5.extendedFrags_uniqNB2FC.txt

Examples

FC <- getFC()
dim(FC)

cpanse/NestLink documentation built on May 16, 2022, 2:33 a.m.