Description Usage Arguments Details Value Author(s) Examples

Combine the technical replicates of Cq values and amplification efficiencies on the basis
of mean, median and geometric mean and compute standard deviation of Cq and efficiency within the replicates
in object of class `"RTqPCRBatch"`

.

1 2 3 | ```
## S4 method for signature 'RTqPCRBatch'
CombineTechReps(RTqPCRBatch, calc = "Mean",
cRepCq = TRUE, ...)
``` |

`RTqPCRBatch` |
Object of class |

`calc` |
Which methods to be used out of Mean, Median and Geometric mean. |

`cRepCq` |
if TRUE, then combine replicates in Cq. If FALSE, then combine replicates in amplification efficiencies. |

`...` |
Other parameters to be passed to downstream methods. |

See the vignettes in RTqPCR package.

Object of class `"RTqPCRBatch"`

with new slots.

Navneet Phogat, Matthias Kohl, Matthias.Kohl@stamats.de

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 39 40 41 42 43 44 45 46 47 48 49 50 51 52 53 54 55 56 57 58 59 60 61 62 | ```
## Read in the raw fluorescent data
LC480.example <- file.path(path, "LC480_Example.txt")
cycData.LC480 <- read.RTqPCR(LC480.example, PCRtype = "LC480")
## Read in the sample information data
SampleInfoLC480 <- file.path(path, "LC480_example_SampleInfo.txt")
samInfoLC480 <- read.RTqPCRSampleInfo(SampleInfoLC480, PCRtype = "LC480")
## Merge the fluorescence and sample information data through merge function
merge.LC480<-merge(cycData.LC480,samInfo.LC480)
## Compute the Cq values and amplification efficiencies
Cqeffs.LC480 <- CqValues(merge.LC480, PCRtype = "LC480", Effmethod = "sigfit", baseline = "none")
Cqeffs.LC480 #To see the overview of data
exprs(Cqeffs.LC480)[1:5] ##to visualise the first five CqValues
effs(Cqeffs.LC480)[1:5] ##to visualise the first five amplification efficiencies
exprs(Cqeffs.LC480) ##to visualise all Cq values
effs(Cqeffs.LC480) ##to visualise all amplification efficiencies
## Implement the functions ReplaceNAs, ReplaceAboveCutOff, ReplaceValue and NonDetects as per requirement.
## Combine technical replicates - In this example, we are combining the replicates directly from
## the output of CqValues function
## replicates can be combined through following three methods
## 1) based on mean (default method is for Cq values and is based on mean)
## i) combine Cq values and compute the standard deviation of Cq values within replicates
Cqreps <- CombineTechReps(Cqeffs.LC480)
Cqreps ## to visualise the overview of the rsulting data
ii) combine amplification efficiencies and compute the standard deviation of amplification efficiencies
within replicates
effsreps <- CombineTechReps(Cqeffs.LC480, cRepCq = FALSE)
## 2) Based on median
## i) Combine Cq values and compute standard deviation of Cq values within replicates
Cqreps2 <- CombineTechReps(Cqeffs.LC480, calc = "Median")
ii) Combine amplification efficiencies and compute their standard deviation within replicates
effsreps2 <- CombineTechReps(Cqeffs.LC480, calc = "Median", cRepCq = FALSE)
## 3) Based on Geometric Mean
## i) combine Cq values and compute their standard deviation within replicates
Cqreps3 <- CombineTechReps(Cqeffs.LC480, calc = "Geom")
ii) combine amplification efficiencies and compute their standard deviation within replicates
effsreps <- CombineTehcReps(Cqeffs.LC480, calc = "Geom", cRepCq = FALSE)
``` |

Embedding an R snippet on your website

Add the following code to your website.

For more information on customizing the embed code, read Embedding Snippets.