Fraction of signal in features

Identical to its reference in the validationFRiP, as the ENCODE guidelines define it (Landt et al. 2012). doi:10.1101/gr.136184.111

In the app

Analysis panel, under 1D tasks: Fraction of signal in features

Command

chromosomix frip

Reads

Tracks and interval files, with or without a contact map

Also known as

FRiP, reads in peaks, enrichment

Fraction of signal in features is FRiP, the fraction of reads in peaks, taken of any loaded track: the share of its signal inside a set of intervals, beside the share of the genome the set covers. Their ratio, the enrichment, is the column to read. Use it to check a library against its peaks, or to rank tracks against a set.

Running it

Load one or more tracks and a feature set (Tracks and features). Open Fraction of signal in features on the 1D tasks card of the Analysis panel, tick the tracks and choose the features; no map is needed. The drawer shows a row per track, the strongest enrichment first.

The same run from a shell:

chromosomix frip [<map>] --tracks <tracks.bw> --features <features.bed> [--<parameter> <value> …] --out <dir>

Parameters

read features at 0, the default, reads about 50 samples across a feature of the set’s median width. score every feature adds a table with each feature’s signal, mean and share of the track’s total, which shows whether the FRiP belongs to the set or to a handful of its features.

Parameter	Takes	Default	What it does
tracks--tracks <file,…>	files: a signal track	—	—
features--features <file>	a file: a feature set	—	—
read features at--resolution <n>	a whole number, at least 0, in bp	0	0 is auto: about 50 samples across a feature of the set’s median width.
score every feature--perFeature / --no-perFeature	on or off	off	One row per feature, so a FRiP carried by a handful of them can be seen to be.

What it writes

• table: a table: TSV

On the command line every file goes into --out as <file stem>.frip.<output>.<ext>, and each TSV opens with # lines naming the build, the file and every parameter that produced it.

Reading the result

• FRiP: the signal inside the set over the signal everywhere. Signal is an area, value × bases, so a wide feature weighs by its width.
• Genome covered: the set’s bases over the assembly’s.
• Enrichment: FRiP over genome covered. 1 is a track with no preference for the set: 30 % of the signal in 30 % of the genome. The same 30 % in half a per cent of the genome is a sixtyfold enrichment.
• Signal inside and Signal total: the two areas.
• Set with data: the share of the set’s bases the track has any value for. A low one means the FRiP is about a small part of the set.

The features are merged first, so a base two of them share, as transcripts of one gene do, counts once; the table’s title gives the number of merged features. The whole track is read from a zoom level where the file has one fine enough, and the note gives both resolutions.

Compared with ENCODE’s FRiP

This is the ENCODE guidelines’ FRiP, of a track’s signal rather than of reads. In the validation, reading the whole track from a zoom level moves a FRiP by less than the last of its four decimals.