formatCheck: Check the format of the uploaded gene list or ranked gene...

Description Usage Arguments Value Author(s) Examples

View source: R/formatCheck.R

Description

The formatCheck function can check the format of the gene list or ranked gene list file or object uploaded to the WebGestaltR for the analysis.

Usage

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formatCheck(dataType="list", inputGeneFile=NULL,inputGene=NULL)

Arguments

dataType

Currently, the formatCheck function supports 2 data type: 1. "list" means the uploaded file or data is a gene list 2. "rnk" means the uploaded file or data is a ranked gene list with two columns (genes and scores).

inputGeneFile

The uploaded data file. If the dataType is "list", the file extension should be "txt" and have only one column. If the dataType is "rnk", the file extension should be "rnk" and have two columns (genes and scores).

inputGene

The uploaded R object. If the dataType is "list", the R object should be a vector. If the dataType is "rnk", the R object should be a data.frame and have two columns (genes and scores).

Value

The formatCheck function will return error if the data format is incorrect. Otherwise, it will return the processed data for the analysis.

Author(s)

Jing Wang

Examples

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geneFile<-system.file("extdata","interestingGenes.txt",package="WebGestaltR")
interestGene<-formatCheck(dataType="list",inputGeneFile=geneFile,inputGene=NULL)

Example output

Initialize Python Version 2.7.6 (default, Oct 26 2016, 20:33:43) 
[GCC 4.8.4]

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*          Welcome to WebGestaltR !      *

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WebGestaltR documentation built on May 30, 2017, 8:17 a.m.