In USCbiostats/pfamscanr: An R client for EMBL-EBI's PfamScan API

knitr::opts_chunk$set(
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  fig.path = "man/figures/README-",
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pfamscanr

The goal of pfamscanr is to ...

Installation

You can download the development version from GitHub with:

# install.packages("devtools")
devtools::install_github("USCbiostats/pfamscanr")

Example

This is an example extracted directly from the website https://www.ebi.ac.uk/Tools/pfa/pfamscan/

library(pfamscanr)
ans <- pfamscan(
  fasta_str = ">sp|P35858|ALS_HUMAN OS=Homo sapiens GN=IGFALS PE=1 SV=1
  MALRKGGLALALLLLSWVALGPRSLEGADPGTPGEAEGPACPAACVCSYDDDADEL
  SVFCSSRNLTRLPDGVPGGTQALWLDGNNLSSVPPAAFQNLSSLGFLNLQGGQLGS
  LEPQALLGLENLCHLHLERNQLRSLALGTFAHTPALASLGLSNNRLSRLEDGLFEG
  LGSLWDLNLGWNSLAVLPDAAFRGLGSLRELVLAGNRLAYLQPALFSGLAELRELD
  LSRNALRAIKANVFVQLPRLQKLYLDRNLIAAVAPGAFLGLKALRWLDLSHNRVAG
  LLEDTFPGLLGLRVLRLSHNAIASLRPRTFKDLHFLEELQLGHNRIRQLAERSFEG
  LGQLEVLTLDHNQLQEVKAGAFLGLTNVAVMNLSGNCLRNLPEQVFRGLGKLHSLH
  LEGSCLGRIRPHTFTGLSGLRRLFLKDNGLVGIEEQSLWGLAELLELDLTSNQLTH
  LPHRLFQGLGKLEYLLLSRNRLAELPADALGPLQRAFWLDVSHNRLEALPNSLLAP
  LGRLRYLSLRNNSLRTFTPQPPGLERLWLEGNPWDCGCPLKALRDFALQNPSAVPR
  FVQAICEGDDCQPPAYTYNNITCASPPEVVGLDLRDLSEAHFAPC",
  email = "[e-mail]",
  httr::config(connecttimeout=60)
)

data("P35858", package="pfamscanr")
ans <- P35858

ans

USCbiostats/pfamscanr documentation built on Dec. 31, 2020, 5:37 p.m.