deltas: Calculate Fold Changes for RT-qPCR Data
In obenlan2/DoubleDelta: Calculations for the Double Delta Ct Method

Description Usage Arguments Value See Also Examples

The Ct values from a specified gene of interest (GOI) for two specified treatments will be extracted, the mean Ct for both treatments will be calculated, and the delta Ct value between the treatments will be calculated. The same will be done for a specified reference gene(s). This function can normalize the GOI delta Ct with up to three reference genes. The delta Ct of the reference gene(s) will be used to normalize the delta Ct of the GOI and generate the double delta Ct. The double delta Ct will be used to calculate the fold change. Delta and double delta Cts for the GOI and the reference gene(s) will be printed along with the fold change which will be returned at the end of the function.

1	deltas(data, gene_name, time_point, treatment1, treatment2, control_gene, control_gene2 = FALSE, control_gene3 = FALSE)

`data`	This is a data frame imported from a CSV file containing RT-qPCR results generated from SDS 2.3 software or a data frame generated from the Read_Combine_Quality function.
`gene_name`	The name of the user's GOI. Needs to be in quotes.
`time_point`	The name of the user's time-point of interest. Needs to be in quotes.
`treatment1`	The name of the user's treatment being compared to treatment2. The name needs to be in quotes.
`treatment2`	The name of the user's treatment being compared to treatment1. The name needs to be in quotes.
`control_gene`	The name of one control gene used in the experiment. Needs to be in quotes.
`control_gene2`	The name of the second control gene used in the experiment. Needs to be in quotes. Default value is FALSE.
`control_gene3`	The name of the third control gene used in the experiment. Needs to be in quotes. Default value is FALSE.

Delta and double delta Cts for the GOI and the reference gene(s) will be printed along with the fold change in order to view results of the calculations. However, the fold change (which is in the numeric class) is the only value returned with the return function and qwhen pointing the function to a name, the fold change will be the only value that will be associated with the given name.

Read_Combine_Quality combine_folds

mypath <- system.file("extdata", "example1.csv", package = "DoubleDelta")
data <- read.csv(mypath)
#Using three reference genes
deltas(data, "Gene1", "12HAT", "UT", "ST", "BTUB", "GTPB", "GAPDH")
#Using two reference genes
deltas(data, "Gene1", "12HAT", "UT", "ST", "BTUB", "GTPB")
#Using one reference gene
deltas(data, "Gene1", "12HAT", "UT", "ST", "BTUB")