Description Usage Arguments Details Value References Examples

View source: R/assessment_fun.R

Uses the *C_T* values from a serial dilution experiment to calculate the
a curve for each gene and the log of the input amount

1 | ```
pcr_standard(df, amount, plot = FALSE)
``` |

`df` |
A data.frame of |

`amount` |
A numeric vector of the input amounts or dilutions. The length of this vector should equal the row number of df |

`plot` |
A logical (default FALSE) to indicate whether to return a data.frame or a plot |

Fortunately, regardless of the method used in the analysis of qPCR data, The quality assessment are done in a similar way. It requires an experiment similar to that of calculating the standard curve. Serial dilutions of the genes of interest and controls are used as input to the reaction and different calculations are made. Curves are required for each gene using the $C_T$ value and the log of the input amount. In this case, a separate slope and intercept are required for the calculation of the relative expression when applying the standard curve model.

When plot is FALSE returns a data.frame of 4 columns describing the
line between the *C_T* of each gene and the log of amount

gene The column names of df

intercept The intercept of the line

slope The slope of the line

r_squared The squared correlation

When plot is TRUE returns a graph instead shows the average and
standard deviation of of the *C_T* at different input amounts.

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.

1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 | ```
# locate and read file
fl <- system.file('extdata', 'ct3.csv', package = 'pcr')
ct3 <- read.csv(fl)
# make amount/dilution variable
amount <- rep(c(1, .5, .2, .1, .05, .02, .01), each = 3)
# calculate the standard curve
pcr_standard(ct3,
amount = amount)
# plot the standard curve
pcr_standard(ct3,
amount = amount,
plot = TRUE)
``` |

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