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https://github.com/ramiromagno/sisti
Real-Time PCR Data Sets by Sisti et al. (2010)
https://github.com/ramiromagno/sisti
qpcr r
Last synced: 21 days ago
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Real-Time PCR Data Sets by Sisti et al. (2010)
- Host: GitHub
- URL: https://github.com/ramiromagno/sisti
- Owner: ramiromagno
- License: cc-by-4.0
- Created: 2024-04-26T23:44:39.000Z (8 months ago)
- Default Branch: main
- Last Pushed: 2024-04-28T02:17:21.000Z (8 months ago)
- Last Synced: 2024-11-27T21:38:24.434Z (about 1 month ago)
- Topics: qpcr, r
- Language: R
- Homepage: https://rmagno.eu/sisti/
- Size: 4.43 MB
- Stars: 0
- Watchers: 1
- Forks: 0
- Open Issues: 0
-
Metadata Files:
- Readme: README.Rmd
- License: LICENSE.md
Awesome Lists containing this project
README
---
output: github_document
---
```{r, include = FALSE}
knitr::opts_chunk$set(
collapse = TRUE,
comment = "#>",
fig.path = "man/figures/README-",
out.width = "100%",
dpi = 400
)
```
# sisti
[](https://CRAN.R-project.org/package=sisti)
[](https://github.com/ramiromagno/sisti/actions/workflows/R-CMD-check.yaml)
`{sisti}` provides real-time PCR data sets by Sisti et al. (2010) in tidy
format as one single table (also named) `sisti`.
The primary dataset comprises a ten-fold dilution series spanning copy numbers
from $3.14 \times 10^7$ to $3.14 \times 10^2$, with twelve replicates per
concentration. These samples are based on a pGEM-T Promega plasmid containing a
104 bp fragment of the mitochondrial gene NADH dehydrogenase 1 (MT-ND1),
amplified using the ND1/ND2 primer pair. The remaining three datasets contain
qPCR results in the presence of specific PCR inhibitors: tannic acid,
immunoglobulin G (IgG), and quercetin, respectively, to assess their effects on
the amplification process.
Each original data set can be obtained by filtering `sisti` by `plate` (see
below).
## Installation
``` r
install.packages("sisti")
```
## Data
Each sample group is defined by the inhibitor ("none", "tannic acid", "IgG" or
"quercitin"), respective inhibitor concentration, and initial amplicon copy
number.
```{r}
library(ggplot2)
library(dplyr, warn.conflicts = FALSE)
library(sisti)
sisti |>
dplyr::distinct(plate, inhibitor, inhibitor_conc, copies, dilution) |>
print(n = Inf)
```
Here is the number of replicates per group:
```{r}
sisti |>
dplyr::distinct(plate, inhibitor, inhibitor_conc, copies, dilution, replicate) |>
dplyr::count(plate, inhibitor, inhibitor_conc, copies, dilution) |>
print(n = Inf)
```
### Standard dilution series
Most concentrated set of samples in the dilution series have $3.14 \times 10^7$
copies of the NADH dehydrogenase 1 (MT-ND1) amplicon. Following samples in
the series are ten-fold dilutions.
```{r}
sisti |>
dplyr::filter(plate == "calibration") |>
ggplot(aes(
x = cycle,
y = fluor,
group = interaction(replicate, copies),
col = as.factor(copies)
)) +
geom_line(linewidth = 0.1) +
geom_point(size = 0.05) +
labs(color = "Copy number")
```
### Inhibition by tannic acid
```{r}
sisti |>
dplyr::filter(plate == "tannic acid") |>
ggplot(aes(
x = cycle,
y = fluor,
group = interaction(replicate, inhibitor_conc),
col = as.factor(inhibitor_conc)
)) +
geom_line(linewidth = 0.1) +
geom_point(size = 0.05) +
labs(color = "Tannic acid conc (mg/mL)")
```
### Inhibition by immunoglobulin G (IgG)
```{r}
sisti |>
dplyr::filter(plate == "IgG") |>
ggplot(aes(
x = cycle,
y = fluor,
group = interaction(replicate, inhibitor_conc),
col = as.factor(inhibitor_conc)
)) +
geom_line(linewidth = 0.1) +
geom_point(size = 0.05) +
labs(color = "IgG conc (mg/mL)")
```
### Inhibition by quercitin
```{r}
sisti |>
dplyr::filter(plate == "quercitin") |>
ggplot(aes(
x = cycle,
y = fluor,
group = interaction(replicate, inhibitor_conc),
col = as.factor(inhibitor_conc)
)) +
geom_line(linewidth = 0.1) +
geom_point(size = 0.05) +
labs(color = "Quercitin conc (mg/mL)")
```
## Code of Conduct
Please note that the `{sisti}` project is released with a [Contributor Code of
Conduct](https://rmagno.eu/sisti/CODE_OF_CONDUCT.html). By contributing to this
project, you agree to abide by its terms.
## References
Davide Sisti, Michele Guescini, Marco BL Rocchi, Pasquale Tibollo, Mario D'Atri
and Vilberto Stocchi. _Shape based kinetic outlier detection in real-time PCR_.
BMC Bioinformatics 11:186 (2010). doi:
[10.1186/1471-2105-11-186](https://doi.org/10.1186/1471-2105-11-186).