####======================SeqmanBefore()=======================####
#' @title prepare chip probe information(.txt) before seqman pipelin
#' @description When we want to annotate a chip with probe sequence,Seqman software is a good choice.Before use Seqman,a probe information should be prepared,which SeqmanBefore() can help do.
#' @param eset an eset object containing feature data.
#' @param probe.id.col the colname of the probe id
#' @param sequence.col the colname of the sequence information
#' @param save.file whether save results as rda
#' @param names part of saved file name
#' @return a .txt file containing probe ids and sequeces.
#' @author Weibin Huang<\email{654751191@@qq.com}>
#' @examples
#' load("E:/RCloud/database/DataDownload/GEOqueryDownload/GSE17154/GSE17154_rawEset.rda")
#' probe.id.col="ID"
#' sequence.col = "SEQUENCE"
#' test1 = SeqmanBefore(eset,
#' probe.id.col,
#' sequence.col,
#' save.file=T,
#' names = "test1")
#' @export
SeqmanBefore <- function(eset,
probe.id.col="ID",
sequence.col = "SEQUENCE",
save.file=T,
names = "test1"){
## 从eset中获取注释信息
library(Biobase)
fdata <- fData(eset)
## 提取
probe.ids <- paste(">",as.character(fdata[,"ID"]),sep = "")
seq1 <- as.character(fdata[,sequence.col])
mt <- matrix(rep(0,2*length(probe.ids)),ncol = 1)
mt[seq(1,(nrow(mt)-1),by=2),] <- probe.ids
mt[seq(2,(nrow(mt)),by=2),] <- seq1
## 保存文件
library(readr)
mt <- as.data.frame(mt);
if(save.file==T){
write.table(mt,paste0(names,"_probesequence.txt"),
sep = "\t",quote = F,
col.names = F,row.names = F)
return(mt)
} else {
return(mt)
}
## End
}
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