The hardware and bandwidth for this mirror is donated by dogado GmbH, the Webhosting and Full Service-Cloud Provider. Check out our Wordpress Tutorial.
If you wish to report a bug, or if you are interested in having us mirror your free-software or open-source project, please feel free to contact us at mirror[@]dogado.de.

vermeulen

CRAN status R-CMD-check

{vermeulen} provides the Biomarker data set by Vermeulen et al. (2009) in tidy format.

This data set is for a real-time quantitative PCR experiment that comprises:

Installation

Install {vermeulen} from CRAN:

# Install from CRAN
install.packages("vermeulen")

You can instead install the development version of {vermeulen} from GitHub:

# install.packages("remotes")
remotes::install_github("ramiromagno/vermeulen")

Usage

Because of CRAN size limits the data is not provided at installation time. The data can be retrieved from this GitHub repository after installation with the function get_biomarker_dataset().

library(vermeulen)
library(tibble)
library(dplyr)

# Takes a few seconds (downloading from GitHub...)
biomarker <- as_tibble(get_biomarker_dataset())
biomarker
#> # A tibble: 1,226,880 × 11
#>    plate well  dye   target target_type sample sample_type copies dilution cycle
#>    <fct> <fct> <fct> <fct>  <fct>       <chr>  <fct>        <int>    <dbl> <int>
#>  1 AHCY  A1    SYBR  AHCY   toi         1495   unk             NA       NA     1
#>  2 AHCY  A1    SYBR  AHCY   toi         1495   unk             NA       NA     2
#>  3 AHCY  A1    SYBR  AHCY   toi         1495   unk             NA       NA     3
#>  4 AHCY  A1    SYBR  AHCY   toi         1495   unk             NA       NA     4
#>  5 AHCY  A1    SYBR  AHCY   toi         1495   unk             NA       NA     5
#>  6 AHCY  A1    SYBR  AHCY   toi         1495   unk             NA       NA     6
#>  7 AHCY  A1    SYBR  AHCY   toi         1495   unk             NA       NA     7
#>  8 AHCY  A1    SYBR  AHCY   toi         1495   unk             NA       NA     8
#>  9 AHCY  A1    SYBR  AHCY   toi         1495   unk             NA       NA     9
#> 10 AHCY  A1    SYBR  AHCY   toi         1495   unk             NA       NA    10
#> # ℹ 1,226,870 more rows
#> # ℹ 1 more variable: fluor <dbl>

Types of samples:

count(
  distinct(biomarker, plate, well, sample_type, copies, dilution),
  sample_type,
  copies,
  dilution
)
#> # A tibble: 7 × 4
#>   sample_type copies dilution     n
#>   <fct>        <int>    <dbl> <int>
#> 1 ntc              0      Inf   192
#> 2 std             15    10000   192
#> 3 std            150     1000   192
#> 4 std           1500      100   192
#> 5 std          15000       10   192
#> 6 std         150000        1   192
#> 7 unk             NA       NA 23424

Code of Conduct

Please note that the {vermeulen} project is released with a Contributor Code of Conduct. By contributing to this project, you agree to abide by its terms.

References

  1. Vermeulen et al.. Predicting outcomes for children with neuroblastoma using a multigene-expression signature: a retrospective SIOPEN/COG/GPOH study. The Lancet Oncology 10, 663–671 (2009). doi: 10.1016/S1470-2045(09)70154-8.

  2. Ruijter et al.. Evaluation of qPCR curve analysis methods for reliable biomarker discovery: Bias, resolution, precision, and implications. Methods 59 32–46 (2013). doi: 10.1016/j.ymeth.2012.08.011.

These binaries (installable software) and packages are in development.
They may not be fully stable and should be used with caution. We make no claims about them.
Health stats visible at Monitor.