pcr_analyze {pcr} | R Documentation |
Apply qPCR analysis methods
Description
A unified interface to invoke different analysis methods of qPCR data.
Usage
pcr_analyze(df, method = "delta_delta_ct", ...)
Arguments
df |
A data.frame of |
method |
A character string; 'delta_delta_ct' default, 'delta_ct' or 'relative_curve' for invoking a certain analysis model |
... |
Arguments passed to the methods |
Details
The different analysis methods can be invoked using the
argument method with 'delta_delta_ct' default, 'delta_ct' or
'relative_curve' for the double delta C_T
, delta ct or the standard curve
model respectively. Alternatively, the same methods can be applied by using
the corresponding functions directly: pcr_ddct, pcr_dct or
pcr_curve
Value
A data.frame by default, when plot
is TRUE returns a plot.
For details; pcr_ddct, pcr_dct and pcr_curve.
References
Livak, Kenneth J, and Thomas D Schmittgen. 2001. “Analysis of Relative Gene Expression Data Using Real-Time Quantitative PCR and the Double Delta CT Method.” Methods 25 (4). ELSEVIER. doi:10.1006/meth.2001.1262.
Examples
# applying the delta delta ct method
## locate and read raw ct data
fl <- system.file('extdata', 'ct1.csv', package = 'pcr')
ct1 <- read.csv(fl)
# add grouping variable
group_var <- rep(c('brain', 'kidney'), each = 6)
# calculate all values and errors in one step
pcr_analyze(ct1,
group_var = group_var,
reference_gene = 'GAPDH',
reference_group = 'brain',
method = 'delta_delta_ct')
# return a plot
pcr_analyze(ct1,
group_var = group_var,
reference_gene = 'GAPDH',
reference_group = 'brain',
method = 'delta_delta_ct',
plot = TRUE)
# applying the delta ct method
# make a data.frame of two identical columns
pcr_hk <- data.frame(
GAPDH1 = ct1$GAPDH,
GAPDH2 = ct1$GAPDH
)
# calculate fold change
pcr_analyze(pcr_hk,
group_var = group_var,
reference_group = 'brain',
method = 'delta_ct')
# return a plot
pcr_analyze(pcr_hk,
group_var = group_var,
reference_group = 'brain',
method = 'delta_ct',
plot = TRUE)
# applying the standard curve method
# locate and read file
fl <- system.file('extdata', 'ct3.csv', package = 'pcr')
ct3 <- read.csv(fl)
# make a vector of RNA amounts
amount <- rep(c(1, .5, .2, .1, .05, .02, .01), each = 3)
# calculate curve
standard_curve <- pcr_assess(ct3, amount = amount, method = 'standard_curve')
intercept <- standard_curve$intercept
slope <- standard_curve$slope
# apply the standard curve method
pcr_analyze(ct1,
group_var = group_var,
reference_gene = 'GAPDH',
reference_group = 'brain',
intercept = intercept,
slope = slope,
method = 'relative_curve')
# return a plot
pcr_analyze(ct1,
group_var = group_var,
reference_gene = 'GAPDH',
reference_group = 'brain',
intercept = intercept,
slope = slope,
method = 'relative_curve',
plot = TRUE)