| exp_input {CpmERCCutoff} | R Documentation |
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