MetricFactory {similaRpeak} | R Documentation

## MetricFactory object

### Description

An object which is a interface to calculate all available metrics separately.

The `MetricFactory` object is inspired from the factory design pattern. Only one instance of `MetricFactory` object is necessary to calculate all available metrics for different profiles, as long as the thresholds set in the `MetricFactory` instance are appropriate for the calculation. The thresholds are set during the `MetricFactory` object creation and cannot be changed afterwards. If different thresholds are needed, a new `MetricFactory` object, with the new thresholds, must be instantiated.

### Usage

    MetricFactory

### Format

An object of class `R6ClassGenerator` of length 24.

### Value

The `MetricFactory$new` function returns a `MetricFactory` object which contains the information about the thresholds used to calculate each metric. It can be used, as many times needed, to calculate the specified metrics.

### Constructor

Create a `MetricFactory` object.

`MetricFactory$new(ratioAreaThreshold=1, ratioMaxMaxThreshold=1, ratioIntersectThreshold=1, ratioNormalizedIntersectThreshold=1, diffPosMaxThresholdMinValue=1, diffPosMaxThresholdMaxDiff=100, diffPosMaxTolerance=0.01, spearmanCorrSDThreashold=1e-8)`

- `ratioAreaThreshold` The minimum denominator accepted to calculate the ratio of the area between both profiles. Default = 1.

- `ratioMaxMaxThreshold` The minimum denominator accepted to calculate the ratio of the maximum values between both profiles. Default = 1.

- `ratioIntersectThreshold` The minimum denominator accepted to calculate the ratio of the intersection area of both profiles and the total area. Default = 1.

- `ratioIntersectThreshold` The minimum denominator accepted to calculate the ratio of the intersection area of both profiles and the total area for normalized profiles. Default = 1.

- `diffPosMaxThresholdMinValue` The minimum peak accepted to calculate the metric. Default = 1.

- `diffPosMaxThresholdMaxDiff` The maximum distance accepted between 2 peaks positions in one profile to calculate the metric. Default=100.

- `diffPosMaxTolerance` The maximum variation accepted on the maximum value to consider a position as a peak position. Default=0.01.

- `spearmanCorrSDThreashold` The minimum standard deviation accepted on both profiles to consider to calculate the metric. Default=1e-8.

### Author(s)

Astrid Deschenes

### See Also

- `similarity` for calculating all available metrics between two ChIP-Seq profiles.

- `demoProfiles` for more informations about ChIP-Seq profiles present in the demoProfiles data.

### Examples

    ## Initialized the factory object
    factory = MetricFactory$new(ratioAreaThreshold=100,
        ratioIntersectThreshold=20,
        diffPosMaxTolerance=0.04)

    ## Define 2 ChIP-Seq profiles
    profile1 <- c(1,59,6,24,65,34,15,4,53,22)
    profile2 <- c(15,9,46,44,9,39,27,34,34,4)

    ## Use the factory object to calculate each metric separatly
    ratio_max_max <- factory$createMetric(metricType="RATIO_MAX_MAX",
        profile1, profile2)
    ratio_max_max

    diff_pos_max <- factory$createMetric(metric="DIFF_POS_MAX", profile1,
        profile2)
    diff_pos_max

    ## Example using ChIP-Seq profiles of H3K27ac (DCC accession: ENCFF000ASG)
    ## and H3K4me1 (DCC accession: ENCFF000ARY) from the Encyclopedia of DNA
    ## Elements (ENCODE) for the region
    data(demoProfiles)

    ## Visualize ChIP-Seq profiles
    plot(demoProfiles$chr3.73159773.73160145$H3K27ac, type="l", col="blue",
        xlab="", ylab="", ylim=c(0, 125), main="chr3:73159773-73160145")
    par(new=TRUE)
    plot(demoProfiles$chr3.73159773.73160145$H3K4me1, type="l", col="darkgreen",
        xlab="Position", ylab="Coverage in reads per million (RPM)",
        ylim=c(0, 125))
    legend("topright", c("H3K27ac","H3K4me1"), cex=1.2,
        col=c("blue","darkgreen"), lty=1)

    ## Calculate metrics using factory object
    ratio_norm_intersect <- factory$createMetric(metricType =
        "RATIO_NORMALIZED_INTERSECT",
        profile1=demoProfiles$chr3.73159773.73160145$H3K4me1,
        profile2=demoProfiles$chr3.73159773.73160145$H3K27ac)
    ratio_norm_intersect

    ratio_area <- factory$createMetric(metricType="RATIO_AREA",
        profile1=demoProfiles$chr3.73159773.73160145$H3K4me1,
        profile2=demoProfiles$chr3.73159773.73160145$H3K27ac)
    ratio_area

[Package similaRpeak version 1.26.0 Index]