Calc.Expr: calculate the relative expression

In qPCR.CT: qPCR data analysis and plot package

Description

use control gene and ddCT methods to calculate the difference

Usage

Calc.Expr(filename, con_group_name, tr_group_name, con_gene_name = "18s", tr_gene_name, repeatnum = 3, ...)

Arguments

filename
con_group_name
tr_group_name
con_gene_name
tr_gene_name
repeatnum
...

Author(s)

YZ Pan, XY Yan, JX Li

Examples

##---- Should be DIRECTLY executable !! ----
##-- ==>  Define data, use random,
##--	or do  help(data=index)  for the standard data sets.

## The function is currently defined as
function(filename, con_group_name, tr_group_name, 
                    con_gene_name= "18s",tr_gene_name, 
                    repeatnum = 3, ... )
{
#load data
  rawdata<-read.csv(filename)
#subset data
  unknown<-   subset(rawdata, Type != "NTC")
  num    <-   length(unknown$Type)
  groupnum <- num/repeatnum
  con_group<- subset(unknown, Identifier == con_group_name)
  tr_group <- subset(unknown, Identifier == tr_group_name)
  con_group_con<- subset(con_group, Fluor == con_gene_name)
  tr_group_con <- subset(tr_group, Fluor == con_gene_name)
  con_group_tr <- subset(con_group, Fluor == tr_gene_name)
  tr_group_tr  <- subset(tr_group, Fluor == tr_gene_name)
#read CT value, convert the factors into CT number
  con.con<-con_group_con[6]
  con.con<-as.numeric(paste(con.con[[1]]))
  tr.con<- tr_group_con[6]
  tr.con<- as.numeric(paste(tr.con[[1]]))
  con.tr<- con_group_tr[6]
  con.tr<- as.numeric(paste(con.tr[[1]]))
  tr.tr <- tr_group_tr[6]
  tr.tr <- as.numeric(paste(tr.tr[[1]]))
#calculate 
  cal.CT <- cal_ct(con.con,tr.con,con.tr,tr.tr)
#output data
  names(cal.CT) <- c(con_group_name , tr_group_name)
#return data
  return(cal.CT)

  }

Example output

Loading required package: RColorBrewer
function (filename, con_group_name, tr_group_name, con_gene_name = "18s", 
    tr_gene_name, repeatnum = 3, ...) 
{
    rawdata <- read.csv(filename)
    unknown <- subset(rawdata, Type != "NTC")
    num <- length(unknown$Type)
    groupnum <- num/repeatnum
    con_group <- subset(unknown, Identifier == con_group_name)
    tr_group <- subset(unknown, Identifier == tr_group_name)
    con_group_con <- subset(con_group, Fluor == con_gene_name)
    tr_group_con <- subset(tr_group, Fluor == con_gene_name)
    con_group_tr <- subset(con_group, Fluor == tr_gene_name)
    tr_group_tr <- subset(tr_group, Fluor == tr_gene_name)
    con.con <- con_group_con[6]
    con.con <- as.numeric(paste(con.con[[1]]))
    tr.con <- tr_group_con[6]
    tr.con <- as.numeric(paste(tr.con[[1]]))
    con.tr <- con_group_tr[6]
    con.tr <- as.numeric(paste(con.tr[[1]]))
    tr.tr <- tr_group_tr[6]
    tr.tr <- as.numeric(paste(tr.tr[[1]]))
    cal.CT <- cal_ct(con.con, tr.con, con.tr, tr.tr)
    names(cal.CT) <- c(con_group_name, tr_group_name)
    return(cal.CT)
}

qPCR.CT documentation built on May 30, 2017, 3:51 a.m.