lists_combiner: function combining gene lists, alternative for Venn diagram

In wizbionet/wizbionet: non-coding RNAs data integrator and prioritizer

Description

This function combines multiple gene lists together and summarizes occurrence of the string within a list. Gene lists which will be combined should be a data frame (inputDF) of multiple gene/miRNAslists/or other stings. Gene list in inputDF don't need to have equal length. Output provides logical information if gene (or other string) was present on given list. After using this function you can try to use clusterizer_OneR() on first and last column.

Usage

lists.combiner(inputDF)

Arguments

inputDF

inputDF is a data frame in which each column is a different gene list. Gene lists in inputDF don't need to have equal length or be deduplicated. inputDF need to have headings. It can be imported from txt file

Value

Output provides logical information if gene (or other string) was present on given list, and count of occurrences for each gene.

Author(s)

Zofia Wicik

Examples

#example dataframe with gene lists
options(stringsAsFactors = FALSE)
GeneList1=c('PTGER3','FGFR1','ANO5','SGCD','CCKBR',
'PTGFR','NELL1','TBC1D8B','TGFB3')
GeneList2=c('CDH24','PAX1','PTGER3','TBC1D8B','TGFB3',
'PTGER3','NR2C2','NR2C2')
GeneList3=c('PTGER3','FGFR1','ONECUT2','NEBL','SNTB2',
'USP9Y','KAT6A','CRIM1',
'IGSF10','PRKDC','RAD23B','BRD1','PTPRM','PTGIS','RGS5',
'XIRP1','SPSB4')
GeneList4=c('PTGER3','FGFR1','GLIPR1','BCR','SMARCA2','MSMO1','FGF13','KALRN')
x<- list(GeneList1,	GeneList2, GeneList3,	GeneList4)
inputDF<- cbind_filler	(x)
names(inputDF)<-c('GeneList1',	'GeneList2', 'GeneList3',	'GeneList4' )
inputDF


#run function
output<- wizbionet::lists.combiner(inputDF)
head(output, n=3)

wizbionet/wizbionet documentation built on Sept. 9, 2020, 12:45 a.m.