exp_input: A data frame of expected ERCC1 and ERCC2 ratios

In CpmERCCutoff: Calculation of Log2 Counts per Million Cutoff from ERCC Controls

A data frame of expected ERCC1 and ERCC2 ratios

Description

A data frame that contains the expected spike in ERCC data. This data can be obtained from 'ERCC Controls Analysis' manual located on Thermo Fisher's ERCC RNA Spike-In Mix product [page](https://assets.thermofisher.com/TFS-Assets/LSG/manuals/cms_095046.txt). The 'exp_input' data frame mirrors the fields shown in the ERCC manual. For the LCPM cutoff calculation, the last column of the log2 expected fold change ratios are used. Ensure that this column is titled "expected_lfc_ratio". See the example code below for formatting the data.

Usage

exp_input

Format

A data frame with 92 rows and 4 columns: Each row represents an ERCC transcript. Columns are described below:

ercc_id

ERCC spike-in mRNA Ids (ERCC-00002 – ERCC-00171)

subgroup

ERCC subgroups (A – D)

ercc1_conc

ERCC1 concentration (0.014 – 30,000)

ercc2_conc

ERCC2 concentration (0.007 – 30,000)

expected_fc_ratio

Expected fold change ratio (.5 – 4)

expected_lfc_ratio

Expected log2 fold change ratio (-1 – 2)

Examples

# Order rows by ERCC ID and assign to rownames.
exp_input = exp_input[order(exp_input$ercc_id), ]
rownames(exp_input) = exp_input$ercc_id

CpmERCCutoff documentation built on Sept. 13, 2022, 5:06 p.m.