CTSStagCount: Extract raw CAGE TSSs expression tables from 'CAGEr' objects

Description Usage Arguments Value Author(s) See Also Examples

Description

Extracts the tag count for all detected TSSs in all CAGE datasets from CAGEset and CAGEexp objects.

Usage

 1
 2
 3
 4
 5
 6
 7
 8
 9
10
11
12
13
14
15
16
17
18
19
20
21
22
23
24
25
26
27
28
29
30
31
32
33
34
35
CTSStagCount(object)

## S4 method for signature 'CAGEset'
CTSStagCount(object)

## S4 method for signature 'CAGEexp'
CTSStagCount(object)

CTSStagCountDf(object)

## S4 method for signature 'CAGEset'
CTSStagCountDf(object)

## S4 method for signature 'CAGEexp'
CTSStagCountDf(object)

CTSStagCountDF(object)

## S4 method for signature 'CAGEset'
CTSStagCountDF(object)

## S4 method for signature 'CAGEexp'
CTSStagCountDF(object)

CTSStagCountDA(object)

## S4 method for signature 'CAGEr'
CTSStagCountDA(object)

CTSStagCountGR(object, samples)

## S4 method for signature 'CAGEr'
CTSStagCountGR(object, samples)

CTSStagCountSE(object)

Arguments

object

A CAGEr object.

samples

(For CTSStagCountGR.) Name(s) or number(s) identifying sample(s).

Value

Returns an object with number of CAGE tags supporting each TSS (rows) in every CAGE dataset (columns). The class of the object depends on the function being called:

Author(s)

Vanja Haberle

Charles Plessy

See Also

getCTSS()

Other CAGEr accessor methods: CTSSclusteringMethod, CTSScoordinates, CTSScumulativesTagClusters, CTSSnormalizedTpm, CTSStagCountTable, GeneExpDESeq2, GeneExpSE, genomeName, inputFilesType, inputFiles, librarySizes, sampleLabels, seqNameTotalsSE, tagClusters

Examples

1
2
3
4
5
6
7
8
9

CAGEr documentation built on June 21, 2018, 2 a.m.