cal_ct: caculate CT in PCR

In qPCR.CT: qPCR data analysis and plot package

Description

USE delta delta CT method to calculate the expression differnce ~~

Usage

cal_ct(con.con, tr.con, con.tr, tr.tr)

Arguments

con.con	CT value of control group control gene
tr.con	CT value of treat group control gene
con.tr	CT value of control group target gene
tr.tr	CT value of treat group target gene

Details

These are CT values from the dataset!

Value

If it is a LIST, use

comp1	Description of 'comp1'
comp2	Description of 'comp2'

...

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(con.con, tr.con, con.tr, tr.tr)
{
  #get length of data
  lcc <- length(con.con)
  ltc <- length(tr.con)
  lct <- length(con.tr)
  ltt <- length(tr.tr)
  #check length
  if(lcc == 0 || ltc == 0 || lct == 0 || ltt ==0)
  {
    cat("Invalid dataset! Length of dataset is 0. Please check dataset!")
  } else if ((lcc != ltc) || (lcc != lct) || (lcc!=ltt) || (ltc != lct) || (lct != ltt)) {
    cat("Invalid dataset! The length of dataset is not equal.Please check dataset!")
  } else {
    mean.cc <- mean(con.con)
    mean.tc <- mean(tr.con)
    mean.ct <- mean(con.tr)
    mean.tt <- mean(tr.tr)
    dcon.tr <- con.tr - mean.cc
    dtr.tr  <- tr.tr  - mean.tc
    mean.dcon.tr <- mean(dcon.tr)
    mean.dtr.tr <- mean(dtr.tr)
    ddcon.tr <- dcon.tr - mean.dcon.tr
    ddtr.tr  <- dtr.tr  - mean.dcon.tr
    two.ddcon.tr <- 2^ddcon.tr
    two.ddtr.tr <- 2^ddtr.tr
    mean.two.ddcon.tr <- mean(two.ddcon.tr)
    mean.two.ddtr.tr <- mean(two.ddtr.tr)
    final.con <- two.ddcon.tr / mean.two.ddcon.tr
    final.tr  <- two.ddtr.tr /  mean.two.ddcon.tr
    final <- data.frame(final.con, final.tr)
    return(final)
  }
  }

Example output

Loading required package: RColorBrewer
function (con.con, tr.con, con.tr, tr.tr) 
{
    lcc <- length(con.con)
    ltc <- length(tr.con)
    lct <- length(con.tr)
    ltt <- length(tr.tr)
    if (lcc == 0 || ltc == 0 || lct == 0 || ltt == 0) {
        cat("Invalid dataset! Length of dataset is 0. Please check dataset!")
    }
    else if ((lcc != ltc) || (lcc != lct) || (lcc != ltt) || 
        (ltc != lct) || (lct != ltt)) {
        cat("Invalid dataset! The length of dataset is not equal.Please check dataset!")
    }
    else {
        mean.cc <- mean(con.con)
        mean.tc <- mean(tr.con)
        mean.ct <- mean(con.tr)
        mean.tt <- mean(tr.tr)
        dcon.tr <- con.tr - mean.cc
        dtr.tr <- tr.tr - mean.tc
        mean.dcon.tr <- mean(dcon.tr)
        mean.dtr.tr <- mean(dtr.tr)
        ddcon.tr <- dcon.tr - mean.dcon.tr
        ddtr.tr <- dtr.tr - mean.dcon.tr
        two.ddcon.tr <- 2^ddcon.tr
        two.ddtr.tr <- 2^ddtr.tr
        mean.two.ddcon.tr <- mean(two.ddcon.tr)
        mean.two.ddtr.tr <- mean(two.ddtr.tr)
        final.con <- two.ddcon.tr/mean.two.ddcon.tr
        final.tr <- two.ddtr.tr/mean.two.ddcon.tr
        final <- data.frame(final.con, final.tr)
        return(final)
    }
}

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