getGenesInfo: Collect genes information to one table.

In PolinaPavlovich/CONCLUS: ScRNA-seq workflow CONCLUS - from CONsensus CLUSters to a meaningful CONCLUSion.

Description

The function takes a data frame containing gene symbols and (or) ENSEMBL IDs and returns a data frame with such information as gene name, feature type, chromosome, gene IDs in different annotations, knockout information from MGI, a summary from NCBI and UniProt, and whether or not a gene belongs to GO terms containing proteins on the cell surface or involved in secretion.

Usage

getGenesInfo(genes, databaseDir = system.file("extdata", package =
  "conclus"), groupBy = "clusters", orderGenes = "initial",
  getUniprot = TRUE, silent = FALSE, coresGenes = 20)

Arguments

genes	a data frame with the first column called "geneName" containing gene symbols and (or) ENSEMBL IDs. Other columns are optional. For example, the second column could be "clusters" with the name of the cluster for which the gene is a marker.
databaseDir	a path to the database provided with CONCLUS called "Mmus_gene_database_secretedMol.tsv".
groupBy	a column in the input table used for grouping the genes in the output tables. This option is useful if a table contains genes from different clusters.
orderGenes	if "initial" then the order of genes will not be changed.
getUniprot	boolean, whether to get information from UniProt or not. Default is TRUE. Sometimes, the connection to the website is not reliable. If you tried a couple of times and it failed, select FALSE.
silent	whether to show messages from intermediate steps or not.
coresGenes	maximum number of jobs that the function can run in parallel.

Value

Returns a data frame.

PolinaPavlovich/CONCLUS documentation built on May 10, 2019, 2:42 p.m.