Read_Combine_Quality: Combine RT-qPCR Data in CSV files.

In obenlan2/DoubleDelta: Calculations for the Double Delta Ct Method

Description

Function will combine data from up to three CSV files, remove data that resulted in an undetermined Ct, and warn users if any of the data was flagged as a non-amplified well (NAW).

Usage

Read_Combine_Quality(File1, File2 = FALSE, File3 = FALSE, New_name.csv)

Arguments

File1	A CSV file containing RT-qPCR results generated from SDS 2.3 software.
File2	An additional CSV file containing RT-qPCR results generated from SDS 2.3 software that the user would like to combine with File1. Default value is FALSE.
File3	An additional CSV file containing RT-qPCR results generated from SDS 2.3 software that the user would like to combine with File1 and File2. Default value is FALSE.
New_name.csv	The name the user would like the new file to be called. This should be in quoutes and have the .csv file extension.

Value

This function returns a data frame. Column and row names will be identical to the inputted files and any rows that had "Undetermined" results for the Ct value will be removed. Empty cells will have "NA".

See Also

deltas combine_folds

Examples

data <- system.file("extdata", "example1.csv", package = "DoubleDelta")
data2 <- system.file("extdata", "example2.csv", package = "DoubleDelta")
data3 <- system.file("extdata", "example3.csv", package = "DoubleDelta")

#Making Temporary Files Located in Temp Directory
outfile1 <- tempfile(fileext = "NewFile.csv")
outfile2 <- tempfile(fileext = "NewFile2.csv")
outfile3 <- tempfile(fileext = "NewFile3.csv")


#Run the following code to put "NewFile.csv", "NewFile2.csv", or "NewFile3.csv" in the Temp Directory.

##combining three files
Read_Combine_Quality(File1 = data, File2 = data2, File3 = data3, outfile1)
##combining two files
Read_Combine_Quality(File1 = data, File2 = data2, New_name.csv = outfile2)
##inputing one file
Read_Combine_Quality(File1 = data, New_name.csv = outfile3)

## Not run: 
#Run the following code to view "NewFile.csv", "NewFile2.csv", or "NewFile3.csv" in your designated directory.

##combining three files
Read_Combine_Quality(File1 = data, File2 = data2, File3 = data3, "NewFile.csv")
##combining two files
Read_Combine_Quality(File1 = data, File2 = data2, New_name.csv = "NewFile2.csv")
##inputing one file
Read_Combine_Quality(File1 = data, New_name.csv = "NewFile3.csv")

## End(Not run)

obenlan2/DoubleDelta documentation built on May 5, 2019, 7:10 a.m.