R package For the R Script
Installation should take less than 5 min.
If you want to install the package directly from Github, I recommend to use the devtools package.
library(devtools)
install_github('zhang570221322/R/package_Name')library(devtools)
install_github('zhang570221322/R/mMarker')
library(progress)
library(mMarker)
options(stringsAsFactors = FALSE)
data=read.table("findmarker.xls",header=T,sep="\t")
#Single_cell_markers.txt:wget http://biocc.hrbmu.edu.cn/CellMarker/download/Single_cell_markers.txt
marker_Data=read.table("Single_cell_markers.txt",,header=T,sep="\t")
#input data:findmarker.xls ,marker_Data:Single_cell_markers.txt , topn(20):select var gene , freq(10):maker frequency,topfreqn(4):4,isTopfreqn=T
#output Matrix(cluster1,cluster2,.....)
#description isTopfreqn, if isTopfreqn is true,then the freq of pqrameter is invalid ,and the topfreqn of pqrameter is valid.
match_Marker_data=Get_Cluster_Marker_Matrix(data,marker_Data,topn=20,freq=10,topfreqn=4,isTopfreqn=T)
#match_Marker_data=Get_Cluster_Marker_Matrix(data,marker_Data,topn=20,freq=10,topfreqn=4,isTopfreqn=F)
#match_Marker_data=Get_Cluster_Marker_Matrix(data,markerData)
write.table(match_Marker_data,"out_data.xls",sep="\t")remove.packages("mMarker")None
wlZhang