Package: CpmERCCutoff 1.0.0
Kristen Steenbergen
CpmERCCutoff: Calculation of Log2 Counts per Million Cutoff from ERCC Controls
Implementation of the empirical method to derive log2 counts per million (CPM) cutoff to filter out lowly expressed genes using ERCC spike-ins as described in Goll and Bosinger et.al (2022)<doi:10.1101/2022.06.23.497396>. This package utilizes the synthetic mRNA control pairs developed by the External RNA Controls Consortium (ERCC) (ERCC 1 / ERCC 2) that are spiked into sample pairs at known ratios at various absolute abundances. The relationship between the observed and expected fold changes is then used to empirically determine an optimal log2 CPM cutoff for filtering out lowly expressed genes.
Authors:
CpmERCCutoff_1.0.0.tar.gz
CpmERCCutoff_1.0.0.tar.gz(r-4.7-any)CpmERCCutoff_1.0.0.tar.gz(r-4.6-any)
CpmERCCutoff_1.0.0.tgz(r-4.6-emscripten)
manual.pdf |manual.html✨
DESCRIPTION
card.svg |card.png
CpmERCCutoff/json (API)
| # Install 'CpmERCCutoff' in R: |
| install.packages('CpmERCCutoff', repos = c('https://cran.r-universe.dev', 'https://cloud.r-project.org')) |
This package does not link to any Github/Gitlab/R-forge repository. No issue tracker or development information is available.
Last updated from:53baa9c143. Checks:4 OK. Indexed: yes.
| Target | Result | Time | Files | Syslog |
|---|---|---|---|---|
| linux-devel-x86_64 | OK | 114 | ||
| source / vignettes | OK | 170 | ||
| linux-release-x86_64 | OK | 113 | ||
| wasm-release | OK | 84 |
Exports:getLowLcpmCutoff
Dependencies:
Readme and manuals
Help Manual
| Help page | Topics |
|---|---|
| A data frame of expected ERCC1 and ERCC2 ratios | exp_input |
| Function to empirically determine a log2 CPM cutoff based on ERCC RNA spike-in | getLowLcpmCutoff |
| A data frame containing sample-level ERCC meta data | mta_dta |
| A data frame of observed spike in ERCC normalized LCPM data | obs_input |
| Plot the empirically derived LCPM cutoff | plot.empLCPM |
| Print the empirically derived LCPM cutoff results | print.empLCPM |
| Summarizing the empirically derived LCPM cutoff | summary.empLCPM |