erccSpikeConcentration: erccSpikeConcentration

In charles-plessy/smallCAGEqc: ad-hoc QC functions for shallow-sequenced test CAGE libraries

Description

Various data related to ERCC spikes

Usage

  erccSpikeConcentration(file = "http://tools.thermofisher.com/content/sfs/manuals/cms_095046.txt")

Arguments

file	File name or URL where to find the ‘cms_095046.txt’ text file. Defaults to the current URL on the Thermo Fisher website.

Details

In quantitative transcriptome analysis, we often add synthetic RNA to the reaction for quality control and normalisation, and the External RNA Controls Consortium (ERCC) spikes are a popular choice, available commercially from Invitrogen (now Thermo Fisher). In the commercial product, the spikes have different concentrations, covering six orders of magnitude. These concentrations are given in a text file on the vendor's webiste, and I do not know if the file is freely redistributable, hence this function to retreive the data from the Internet or a local file.

Value

A data frame representing the file ‘cms_095046.txt’ from the vendors website.

The original column names are ‘Re-sort ID’, ‘ERCC ID’, ‘subgroup’, ‘concentration in Mix 1 (attomoles/ul)’, ‘concentration in Mix 2 (attomoles/ul)’, ‘expected fold-change ratio’, ‘log2(Mix 1/Mix 2)’, but this not fit well for a R data frame. Therefore, they are renamed as: ‘sortID’, ‘erccID’, ‘subgroup’, ‘concMix1’, ‘concMix2’, ‘FC’, ‘log2FC’.

See Also

loadMoiraiStats

charles-plessy/smallCAGEqc documentation built on May 13, 2019, 3:31 p.m.