Title: | qPCR Ct Values to Expression Values |
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Description: | Computes normalized cycle threshold (Ct) values (delta Ct) from raw quantitative polymerase chain reaction (qPCR) Ct values and conducts test of significance using t.test(). Plots expression values based from log2(2^(-1*delta delta Ct)) across groups per gene of interest. Methods for calculation of delta delta Ct and relative expression (2^(-1*delta delta Ct)) values are described in: Livak & Schmittgen, (2001) <doi:10.1006/meth.2001.1262>. |
Authors: | Wilson Jr. Aala |
Maintainer: | Wilson Jr. Aala <[email protected]> |
License: | GPL-3 |
Version: | 0.1.0 |
Built: | 2024-12-07 06:52:57 UTC |
Source: | CRAN |
Computes nomalized Ct values (delta Ct) from raw qPCR Ct values and conducts test of significance using t.test. Plots expression values based from log2(2^(-1*delta delta Ct)) across groups per gene of interest.
qPCRhelper(data.dir = NULL, ref.gene = NULL, ref.group = NULL, plot.ref.group = NULL, plot.nrow = 1, plot.title = NULL)
qPCRhelper(data.dir = NULL, ref.gene = NULL, ref.group = NULL, plot.ref.group = NULL, plot.nrow = 1, plot.title = NULL)
data.dir |
file path. |
ref.gene |
string: value should be one of column names in input table. Used for delta Ct computation. |
ref.group |
string: value should be one of 'Group' values in input table. Used for delta delta Ct computation. |
plot.ref.group |
string: value should be one of 'Group' values in input table. Used to set reference in plotting. |
plot.nrow |
numeric: optional. Number of rows for plotting n number of plots corresponding to n number of genes. |
plot.title |
plot title: optional. |
A dataframe with columns for normalized Ct values (dCt), and gene expression (log2RelExp).
If gene names start with a number, e.g. 18S, please precede the gene name with 'X' without space, e.g.:18S -> X18S
Wilson Jr. Aala
## Create sample table with expected 'Sample', 'Group', and gene Ct columns Sample <- c("C1", "C2", "T1", "T2") #required column Group <- c("C", "C", "T", "T") #required column # Gene Ct values, at least two columns: one reporter, one target gene GAPDH <- c(18.1,18.2,18.1,18.2) #reporter, ref.gene IL4 <- c(30.1,30.5,20.1,20.2) #target a <- data.frame(Sample,Group,GAPDH,IL4) #export using write.table(a,...) ## Write the data frame to a file in a temporary directory temp_file <- file.path(tempdir(), "a.txt") write.table(a, file = temp_file, sep = "\t") ## Run qPCRhelper directly on the file library(qPCRhelper) b <- qPCRhelper(data.dir=temp_file, ref.gene="GAPDH", ref.group="C", plot.ref.group="C", plot.nrow=1, plot.title="My cool qPCR data")
## Create sample table with expected 'Sample', 'Group', and gene Ct columns Sample <- c("C1", "C2", "T1", "T2") #required column Group <- c("C", "C", "T", "T") #required column # Gene Ct values, at least two columns: one reporter, one target gene GAPDH <- c(18.1,18.2,18.1,18.2) #reporter, ref.gene IL4 <- c(30.1,30.5,20.1,20.2) #target a <- data.frame(Sample,Group,GAPDH,IL4) #export using write.table(a,...) ## Write the data frame to a file in a temporary directory temp_file <- file.path(tempdir(), "a.txt") write.table(a, file = temp_file, sep = "\t") ## Run qPCRhelper directly on the file library(qPCRhelper) b <- qPCRhelper(data.dir=temp_file, ref.gene="GAPDH", ref.group="C", plot.ref.group="C", plot.nrow=1, plot.title="My cool qPCR data")