Counts Per Million
Convert raw feature counts into counts per million mapped reads.
Description
CPM scales counts by a supplied mapped-library denominator.
CPM scales counts by a supplied mapped-library denominator. It does not correct for feature length, and its sum reflects whether the supplied features exhaust that denominator.1
Convert raw feature counts into counts per million mapped reads.
When to use Counts Per Million
Use this tool to convert raw feature counts into counts per million mapped reads.
Prepare the upstream counts, expression values, sequences or record lists requested by this tool. Keep corresponding features in the same order and confirm count units, transformations and caller-selected criteria.
How to use Counts Per Million and understand its results
- Prepare the upstream counts, expression values, sequences or record lists requested by this tool. Keep corresponding features in the same order and confirm count units, transformations and caller-selected criteria.
- Enter rawCounts, libraryMappedReads using the field table and calculation rules, then run the tool.
- Read cpm, cpmSum. The explanation below defines the units, signs, ordering and any flags or placeholder values.
- If the tool reports an input issue, correct the values and run it again. Apply the stated assumptions when interpreting a successfully returned result.
| Input field | Meaning | Value type; see rules below | Requirement |
|---|---|---|---|
| rawCounts | Raw counts | list of number | Required |
| libraryMappedReads | Library mapped reads | number | Required |
Enter nonempty nonnegative feature counts and positive mapped-library total. Return CPM in input order and summed CPM. Zero feature counts are accepted; the sum is not forced to one million.
CPM_i=10⁶ rawCount_i/libraryMappedReads Units, indexing, boundary conditions and exceptional cases are defined in the calculation rules above.
| Output field | Meaning | Value type |
|---|---|---|
| cpm | Cpm | list of number |
| cpmSum | Cpm sum | number |
{
"input": {
"rawCounts": [
10,
20
],
"libraryMappedReads": 1000000
},
"output": {
"cpm": [
10,
20
],
"cpmSum": 30
}
}Limitations and assumptions
No library counting, composition correction or length normalization is performed. The calculator does not check that feature counts sum to or lie below the denominator.
Numeric inputs must be finite. Follow the calculation-specific rules for overflow, underflow and exceptional cases. Lists are limited to 100,000 entries; the rules above may require smaller limits. Missing required fields, extra fields, wrong value types and violations of the calculation rules are input errors.
Alternative or Complementary methods
Use Reads Per Kilobase Million: Calculate reads per kilobase of gene per million mapped reads. For a complementary task, use Transcripts Per Million: Normalize transcript length-adjusted abundances to one million TPM.
References
-
Counts Per Million — tool.io
Similar or alternative tools
- Reads Per Kilobase Million
Calculate reads per kilobase of gene per million mapped reads.
- Transcripts Per Million
Normalize transcript length-adjusted abundances to one million TPM.