annotate.results: Annotate prioritised SNVs

In lgl15/cnmtf: Prioritisation of single nucleotide variants using Corrected non-negative matrix tri-factorisation

Description

Function to map SNVs to genes and retrieve functional annotations from DAVID

Usage

annotate.results(name.exp = NULL, snps.known = NULL, snps.known2 = NULL,
  add.david.annotations = TRUE, email.david = NULL,
  add.ensemble.conseq = FALSE, work.dat = NULL, tmap = NULL,
  file.LD = NULL, ld.tao = 0.8)

Arguments

snps.known2	List of known associations
add.david.annotations	Logical. Use DAVID web service or export/import manually
email.david	Email account registered in DAVID.
lconsortiums	List of data consortiums to merge
ltrait.project	List of traits to merge
explore.gwas	Logical. Explore mutations from GWAS cataloge

Value

• cdav.all Chart of annotations from DAVID. Printed to file "summary_david_chart.txt"

• tsa.all Table of annotations from DAVID. Printed to file "summary_david_table.txt"

• tmut.all Table merging annotations for a list of consortiums and traits. Printed to file "summary_david_table_genes.txt"

• tres Final table with metadata for all SNVs. Printed to file "explore_results.csv"

Author(s)

Luis G. Leal, [e-mail]

lgl15/cnmtf documentation built on May 28, 2019, 6:33 p.m.