十年的生信

setwd("C:/Users/daizao/Desktop/Single_Cell_Annotation")
library(magrittr)
library(vroom)
library(tidyverse)
library(clusterProfiler)
library(DT)
library(org.Hs.eg.db)
library(hash)

#cell-marker <- vroom("http://bio-bigdata.hrbmu.edu.cn/CellMarker/download/Human_cell_markers.txt")
CellMarker <- vroom("Human_cell_markers.txt")
CellMarker_table <- as.data.frame(CellMarker)
cellmarker_unite <-unite(CellMarker_table,"cellMarker",c("tissueType","cancerType","cellName"),sep=",")
temp <- as.tbl(cellmarker_unite)
temp1 <- dplyr::select(temp,cellMarker,geneID)
cell_marker <- mutate(temp1,geneID=strsplit(geneID,","))

#test data
data(geneList, package="DOSE")
gene <- names(geneList[abs(geneList)>2])
result <- enricher(gene, TERM2GENE=cell_marker, minGSSize=1)
bb <- bitr(as.data.frame(result)$geneID,fromType="ENTREZID",toType="SYMBOL",OrgDb="org.Hs.eg.db")
h=hash()
for (i in 1:nrow(bb)){.set(h,keys=bb[i,1],values=bb[i,2])}
dz <- as.data.frame(result)
for (i in 1:nrow(dz)){dz$geneID[i] <- as.list(values(h,as.data.frame(result)$geneID[i]))[[1]]}
DT::datatable(dz)

参考连接：你那一串差异基因，到底是在哪个组织、哪种细胞中富集？

library(pdftools)
rm(list=ls())
options(stringsAsFactors=F)
setwd("C:/Users/daizao/Desktop/pdf_table_read")
dz <- pdf_text("mmc3.pdf")
pdf2table <- function(x){
    process1 <- strsplit(x,"\\r\\n")
    process2 <- lapply(process1,function(x){gsub("\"\\s+(.*?)\\s+(.*?)\\s+(.*?)\\s+(.*?)\\s+(.*?)\"","\\1\t\\2\\3\\4\t\\5",x,perl=T)})
    test <- data.frame(matrix(unlist(process2), nrow=(length(unlist(process2))), byrow=T))
    data <- data.frame()
    for (i in 2:nrow(test)){
        a <- unlist(strsplit(test[i,]," "))
        b <- a[grepl("^[a-zA-Z]",unlist(strsplit(test[i,]," ")))]
        temp1 <- paste(b[2:(length(b)-1)],collapse=" ")
        temp2 <- cbind(b[1],temp1,b[(length(b))])
        data <- rbind(data,temp2)
    }
    return(data)
}
data <- pdf2table(dz)
colnames(data) <- data[1,]
data <- data[-1,]
write.table(data,file="gene.txt",sep="\t",row.names=F,quote=F)