# 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

 `1` ```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

 ``` 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 30 31 32 33 34 35 36 37 38``` ```##---- 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, ...)
{
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.