| Title: | Metrics to estimate a level of similarity between two ChIP-Seq profiles |
|---|---|
| Description: | This package calculates metrics which quantify the level of similarity between ChIP-Seq profiles. More specifically, the package implements six pseudometrics specialized in pattern similarity detection in ChIP-Seq profiles. |
| Authors: | Astrid Deschênes [cre, aut], Elsa Bernatchez [aut], Charles Joly Beauparlant [aut], Fabien Claude Lamaze [aut], Rawane Samb [aut], Pascal Belleau [aut], Arnaud Droit [aut] |
| Maintainer: | Astrid Deschênes <[email protected]> |
| License: | Artistic-2.0 |
| Version: | 1.37.0 |
| Built: | 2024-07-19 10:43:35 UTC |
| Source: | https://github.com/bioc/similaRpeak |
This package is calculating six differents metrics to estimate a level of similarity between two ChIP-Seq profiles.
The similarity function calculates six differents metrics:
RATIO_AREA: The ratio between the areas. The larger value is always divided by the smaller value.
DIFF_POS_MAX: The difference between the maximal peaks positions. The difference is always a positive value.
RATIO_MAX_MAX: The ratio between the maximal peaks values. The larger value is always divided by the smaller value.
RATIO_INTERSECT: The ratio between the intersection area and the total area.
RATIO_NORMALIZED_INTERSECT: The ratio between the intersection area and the total area of two normalized profiles. The profiles are normalized by divinding them by their average value.
SPEARMAN_CORRELATION: The Spearman's rho statistic between profiles.
The function similarity also reports basic information about
each ChIP profile such as the number of positions, the area, the maximum
value and the position of the maximum value.
To learn more about similaRpeak package see: https://github.com/adeschen/similaRpeak/wiki
Astrid Deschenes, Elsa Bernatchez, Charles Joly Beauparlant, Fabien Claude Lamaze, Rawane Samb, Pascal Belleau and Arnaud Droit
Maintainer: Astrid Deschenes <[email protected]>
MetricFactory for using a interface to calculate all
available metrics separately.
similarity for calculating all available metrics
between two ChIP-Seq profiles.
ChIP-Seq profiles of region chr7:61968807-61969730 of two histone post-transcriptional modifications linked to highly active enhancers H3K27ac (DCC accession: ENCFF000ASG) and H3K4me1 (DCC accession: ENCFF000ARY) from the Encyclopedia of DNA Elements (ENCODE) data (Dunham I et al. 2012).
data(chr7Profiles)data(chr7Profiles)
A list with 1 entry. The entry is a list of 2 ChIP-Seq
profiles, one per active enhancer (H3K27ac and H3K4me1).The 2 ChIP-Seq
profiles are of identical length and specific to a genomic region. Each
ChiP-Seq profile is a numerical vector containing the profiles values
at each position, as reported in reads per million (RPM).
chr7Profiles a list containing all demo ChIP-Seq
profiles
chr7Profiles$chr7.61968807.61969730 a list containing
2 ChIP-Seq profiles for the genomic region chr7:6196880-61969730
demoProfiles$chr7.61968807.61969730$H3K27ac a numeric vector
containing the profiles values related to the enhancer H3K27ac, as reported
in reads per million (RPM). The first entry of the vector is for position
chr7:61968807 while the last entry is for position chr7:61969730
demoProfiles$chr7.61968807.61969730$H3K4me1 a numeric vector
containing the profiles values related to the enhancer H3K4me1, as reported
in reads per million (RPM). The first entry of the vector is for position
chr7:61968807 while the last entry is for position chr7:61969730
The Encyclopedia of DNA Elements (ENCODE) (DCC accession: ENCFF000MZT)
Dunham I, Kundaje A, Aldred SF, et al. An integrated encyclopedia of DNA elements in the human genome. Nature. 2012 Sep 6;489(7414):57-74.
demoProfiles ChIP-seq profiles related to enhancers
H3K27ac and H3K4me1 (for demonstration purpose)
MetricFactory for using a interface to calculate all
available metrics separately.
similarity for calculating all available metrics
between two ChIP-Seq profiles.
data(chr7Profiles) ## Calculating all metrics for the "chr7.61968807.61969730" region metrics <- similarity(chr7Profiles$chr7.61968807.61969730$H3K4me1, chr7Profiles$chr7.61968807.61969730$H3K27ac, ratioAreaThreshold=10, ratioMaxMaxThreshold=4, ratioIntersectThreshold=5, ratioNormalizedIntersectThreshold=2, diffPosMaxThresholdMinValue=10, diffPosMaxThresholdMaxDiff=100, diffPosMaxTolerance=0.10) metrics ## You can refer to the vignette to see more examples using ChIP-Seq profiles ## extracted from the Encyclopedia of DNA Elements (ENCODE) data.data(chr7Profiles) ## Calculating all metrics for the "chr7.61968807.61969730" region metrics <- similarity(chr7Profiles$chr7.61968807.61969730$H3K4me1, chr7Profiles$chr7.61968807.61969730$H3K27ac, ratioAreaThreshold=10, ratioMaxMaxThreshold=4, ratioIntersectThreshold=5, ratioNormalizedIntersectThreshold=2, diffPosMaxThresholdMinValue=10, diffPosMaxThresholdMaxDiff=100, diffPosMaxTolerance=0.10) metrics ## You can refer to the vignette to see more examples using ChIP-Seq profiles ## extracted from the Encyclopedia of DNA Elements (ENCODE) data.
ChIP-Seq profiles of region chr7:61968807-61969730 of two histone post-transcriptional modifications linked to highly active enhancers H3K27ac (DCC accession: ENCFF000ASG) and H3K4me1 (DCC accession: ENCFF000ARY) from the Encyclopedia of DNA Elements (ENCODE) data (Dunham I et al. 2012).
data(demoProfiles)data(demoProfiles)
A list with 1 entry. The entry is a list of 2
ChIP-Seq profiles, one per active enhancer (H3K27ac and H3K4me1).The 2
ChIP-Seq profiles are of identical length and specific to a
genomic region. Each ChiP-Seq profile is
a numerical vector containing the profiles values at each position, as
reported in reads per million (RPM).
demoProfiles a list containing all demo ChIP-Seq
profiles
demoProfiles$chr2.70360770.70361098 a list containing 2
ChIP-Seq profiles for the genomic region chr2:70360770-70361098
demoProfiles$chr2.70360770.70361098$H3K27ac a numeric vector
containing the profiles values related to the enhancer H3K27ac, as reported
in reads per million (RPM). The first entry of the vector is for position
chr1:70360770 while the last entry is for position chr2:70361098
demoProfiles$chr2.70360770.70361098$H3K4me1 a numeric vector
containing the profiles values related to the enhancer H3K4me1, as reported
in reads per million (RPM). The first entry of the vector is for position
chr1:70360770 while the last entry is for position chr2:70361098
demoProfiles$chr3.73159773.73160145$H3K4me1 a list containing
2 ChIP-Seq profiles for the genomic region chr3:73159773-73160145
demoProfiles$chr3.73159773.73160145$H3K27ac a numeric vector
containing the profiles values related to the enhancer H3K27ac, as reported
in reads per million (RPM). The first entry of the vector is for position
chr2:73159773 while the last entry is for position chr3:73160145
demoProfiles$chr3.73159773.73160145$H3K4me1 a numeric vector
containing the profiles values related to the enhancer H3K4me1, as reported
in reads per million (RPM). The first entry of the vector is for position
chr3:73159773 while the last entry is for position chr3:73160145
The Encyclopedia of DNA Elements (ENCODE) (DCC accession: ENCFF000MZT)
Dunham I, Kundaje A, Aldred SF, et al. An integrated encyclopedia of DNA elements in the human genome. Nature. 2012 Sep 6;489(7414):57-74.
chr7Profiles ChIP-Seq profiles of region
chr7:61968807-61969730 related to enhancers H3K27ac and H3K4me1
(for demonstration purpose)
MetricFactory for using a interface to calculate all
available metrics separately.
similarity for calculating all available metrics
between two ChIP-Seq profiles.
data(demoProfiles) # Calculate metrics for the "chr3:73159773-73160145" region metrics <- similarity(demoProfiles$chr3.73159773.73160145$H3K27ac, demoProfiles$chr3.73159773.73160145$H3K4me1) metrics ## You can refer to the vignette to see more examples using ChIP-Seq profiles ## extracted from the Encyclopedia of DNA Elements (ENCODE) data.data(demoProfiles) # Calculate metrics for the "chr3:73159773-73160145" region metrics <- similarity(demoProfiles$chr3.73159773.73160145$H3K27ac, demoProfiles$chr3.73159773.73160145$H3K4me1) metrics ## You can refer to the vignette to see more examples using ChIP-Seq profiles ## extracted from the Encyclopedia of DNA Elements (ENCODE) data.
An object which is a interface to calculate he difference of profiles maximal peaks positions.
The DiffPosMax object is needed to
calculate the difference of profiles maximal peaks positions.
A threshold and the two profiles are set during the DiffPosMax
object creation. If different thresholds or
profiles are needed, the calculateMetric function should be used,
with the new profiles and thresholds passed as arguments to update those
values inside the DiffPosMax object.
The threshold is the minimum peak value accepted to calculate the ratio.
The thresholdDiff is the maximum distance accepted between two maximum peaks positions in the same profile. When the thresholdDiff is not respected, the profile is considered having more than one peak.
The tolerance is the maximum variation accepted on the maximum peak value to consider a position as a peak position. The tolerance must be between 0 and 1. All peaks within the tolerated range will be considered in the calculation of the metric.
DiffPosMaxDiffPosMax
An object of class R6ClassGenerator of length 24.
The DiffPosMax$new function returns a DiffPosMax
object which contains the information about the two profiles and the
thresholds used to calculate the metric. It can be used, as many times
needed, to calculate the specified metric.
Create a DiffPosMax object.
DiffPosMax$new(profile1, profile2, threshold = 1,
thresholdDiff = 100, tolerance = 0.01)
The threshold is the minimum peak value accepted to calculate the ratio.
The thresholdDiff is the maximum distance accepted between two maximum peaks positions in the same profile. When the thresholdDiff is not respected, the profile is considered having more than one peak.
The tolerance is the maximum variation accepted on the maximum peak value to consider a position as a peak position. All peaks within the tolerated range will be considered in the calculation of the metric.The tolerance must
The DiffPosMax object inherites those functions:
getMetric A function that returns the value of the
calculated metric
getInfo A function that returns a description of the metric
with the metric value.
getType A function that returns the unique name associated
to this metric
calculateMetric A function that modifies the values of the
two profiles and the threshold. The new values (profile1, profile2,
threshold, thresholdDiff, tolerance) are passed as arguments.
Astrid Deschenes
MetricFactory for using a interface to calculate all
available metrics separately or togheter.
Calculate and return the difference between two profiles
maximal peaks positions. The difference is always the first profile value
(profile1 parameter) minus the second profile value (profile2 parameter).
When more than one maximual peak is present in one profile, the mediane of
the position is calculated and used as the maximal peak position.
If one threshold is not respected, the function returns NA.
diffPosMaxMethod(profile1, profile2, threshold = 1, thresholdDist = 100, tolerance = 0.01)diffPosMaxMethod(profile1, profile2, threshold = 1, thresholdDist = 100, tolerance = 0.01)
profile1 |
a |
profile2 |
a |
threshold |
a |
thresholdDist |
a |
tolerance |
a |
The calculated ratio or NA if not all thresholds are
respected.
Astrid Deschenes, Elsa Bernatchez
MetricFactory for using the recommanded interface to
calculate all available metrics separately or togheter.
A class which represents a abstract Metric object which is used to quantify the similarity between two profiles covering the same range.
The Metric class should not be directly instanciated. It should be
used as the parent class of a specific metric class.
MetricMetric
An object of class R6ClassGenerator of length 24.
The Metric$new function returns a Metric
object which contains the information about the two profiles and the
threshold used to calculate the metric. It can be used, as many times
needed, to calculate the specified metric.
Create a Metric object.
Metric$new(profile1, profile2, threshold = NULL)
The Metric object inherites those functions:
getMetric A function that returns the value of the
calculated metric
getInfo A function that returns a description of the metric
with the metric value.
getType A function that returns the unique name associated
to this metric
calculateMetric A function that modifies the values of the
two profiles and the threshold. The new values (profile1, profile2,
threshold) are passed as arguments.
Astrid Deschenes
MetricFactory for using the recommanded interface to
calculate all available metrics separately or togheter.
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.
MetricFactoryMetricFactory
An object of class R6ClassGenerator of length 24.
The MetricFactory$new function returns a MetricFactory
object which contains the information about the thresholds used to calculate
each metric. It can be used, as many times needed, to calculate the
specified metrics.
Create a MetricFactory object.
MetricFactory$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.
Astrid Deschenes
similarity for calculating all available metrics
between two ChIP-Seq profiles.
demoProfiles for more informations about ChIP-Seq
profiles present in the demoProfiles data.
## 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$H3K27ac) ratio_area## Initialized the factory object factory = MetricFactory$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
An object which is a interface to calculate ratio between the profile area of two profiles.
The RatioArea object is needed to
calculate the ratio between the profile area of two profile.
A threshold and the two profiles are set during the RatioArea
object creation. If different threshold or
profiles are needed, the calculateMetric function should be used,
with the new profiles and threshold passed as arguments to update those
values inside the RatioArea object.
The threshold is the minimum profile area value accepted to calculate the ratio.
RatioAreaRatioArea
An object of class R6ClassGenerator of length 24.
The RatioArea$new function returns a RatioArea
object which contains the information about the two profiles and the
threshold used to calculate the metric. It can be used, as many times
needed, to calculate the specified metric.
Create a RatioArea object.
RatioArea$new(profile1, profile2, threshold = 1)
The threshold is the minimum profile area value accepted to calculate the ratio.
The RatioArea object inherites those functions:
getMetric A function that returns the value of the
calculated metric
getInfo A function that returns a description of the metric
with the metric value.
getType A function that returns the unique name associated
to this metric
calculateMetric A function that modifies the values of the
two profiles and the threshold. The new values (profile1, profile2,
threshold) are passed as arguments.
Astrid Deschenes
MetricFactory for using a interface to calculate all
available metrics separately or togheter.
Calculate and return the ratio of profiles area
between two profiles covering the same range. The
area of the first profile is always divided by the area of
the second profile.If one area value is inferior to the threshold, the
function returns NA.
ratioAreaMethod(profile1, profile2, threshold = 1)ratioAreaMethod(profile1, profile2, threshold = 1)
profile1 |
a |
profile2 |
a |
threshold |
a |
The calculated ratio or NA if one profile area value is
inferior to the threshold.
Astrid Deschenes, Elsa Bernatchez
MetricFactory for using the recommanded interface to
calculate all available metrics separately or togheter.
An object which is a interface to calculate the ratio between the peaks values between two profiles.
The RatioIntersect object is needed to
calculate the ratio of profiles intersection area between two profiles and
those profiles total areas.
A threshold and the two profiles are set during the RatioIntersect
object creation. If different threshold or
profiles are needed, the calculateMetric function should be used,
with the new profiles and threshold passed as arguments to update those
values inside the RatioIntersect object.
The threshold is the minimum total area value accepted to calculate a ratio.
RatioIntersectRatioIntersect
An object of class R6ClassGenerator of length 24.
The RatioIntersect$new function returns a
RatioIntersect object which contains the information about the two
profiles and the threshold used to calculate the metric. It can be used, as
many times needed, to calculate the specified metric.
Create a RatioIntersect object.
RatioIntersect$new(profile1, profile2, threshold = 1)
The threshold is the minimum total area value accepted to calculate a ratio.
The RatioIntersect object inherites those functions:
getMetric A function that returns the value of the
calculated metric
getInfo A function that returns a description of the metric
with the metric value.
getType A function that returns the unique name associated
to this metric
calculateMetric A function that modifies the values of the
two profiles and the threshold. The new values (profile1, profile2,
threshold) are passed as arguments.
Astrid Deschenes
MetricFactory for using a interface to calculate all
available metrics separately or togheter.
Calculate and return the ratio between the intersection area
of two profiles and the total area covered by those profiles. If the total
area is inferior to
the threshold, the function returns NA.
ratioIntersectMethod(profile1, profile2, threshold = 1)ratioIntersectMethod(profile1, profile2, threshold = 1)
profile1 |
a |
profile2 |
a |
threshold |
a |
The calculated ratio or NA if the total area is inferior
to the threshold.
Astrid Deschenes, Elsa Bernatchez
MetricFactory for using the recommanded interface to
calculate all available metrics separately or togheter.
An object which is a interface to calculate the ratio between the peaks values between two profiles.
The RatioMaxMax object is needed to
calculate the ratio between
the peaks values between two profiles.
A threshold and the two profiles are set during the RatioMaxMax
object creation. If different threshold or
profiles are needed, the calculateMetric function should be used,
with the new profiles and threshold passed as arguments to update those
values inside the RatioMaxMax object.
The threshold is the minimum peak value accepted to calculate a ratio.
RatioMaxMaxRatioMaxMax
An object of class R6ClassGenerator of length 24.
The RatioMaxMax$new function returns a RatioMaxMax
object which contains the information about the two profiles and the
threshold used to calculate the metric. It can be used, as many times
needed, to calculate the specified metric.
Create a RatioMaxMax object.
RatioMaxMax$new(profile1, profile2, threshold = 1)
The threshold is the minimum peak value accepted to calculate a ratio.
The RatioMaxMax object inherites those functions:
getMetric A function that returns the value of the
calculated metric
getInfo A function that returns a description of the metric
with the metric value.
getType A function that returns the unique name associated
to this metric
calculateMetric A function that modifies the values of the
two profiles and the threshold. The new values (profile1, profile2,
threshold) are passed as arguments.
Astrid Deschenes
MetricFactory for using a interface to calculate all
available metrics separately or togheter.
Calculate and return the ratio of profiles maximal peaks
between two profiles covering the same range. The
maximal peak of the first profile is always divided by the maximal peak of
the second profile.If one peak value is inferior to the threshold, the
function returns NA.
ratioMaxMaxMethod(profile1, profile2, threshold = 1)ratioMaxMaxMethod(profile1, profile2, threshold = 1)
profile1 |
a |
profile2 |
a |
threshold |
a |
The calculated ratio or NA if one peak value is inferior to
the threshold.
Astrid Deschenes, Elsa Bernatchez
MetricFactory for using the recommanded interface to
calculate all available metrics separately or togheter.
An object which is a interface to calculate the ratio of profiles intersection area between two normalized profiles.The profiles are
The RatioNormalizedIntersect object is needed to
calculate the ratio of profiles intersection area between two
normalized profiles.
A threshold and the two profiles are set during the
RatioNormalizedIntersect
object creation. If different profiles are needed, the
calculateMetric function should be used,
with the new profiles passed as arguments to update those
values inside the RatioNormalizedIntersect object.
The threshold is the minimum total normalized area value accepted to calculate a ratio.
RatioNormalizedIntersectRatioNormalizedIntersect
An object of class R6ClassGenerator of length 24.
The RatioNormalizedIntersect$new function returns a
RatioNormalizedIntersect object which contains the information about
the two profiles. It can be used, as many times
needed, to calculate the specified metric.
Create a RatioNormalizedIntersect object.
RatioNormalizedIntersect$new(profile1, profile2, threshold = 1)
The threshold is the minimum total normalized area value accepted to calculate a ratio. Default = 1
The RatioNormalizedIntersect object inherites those functions:
getMetric A function that returns the value of the
calculated metric
getInfo A function that returns a description of the metric
with the metric value.
getType A function that returns the unique name associated
to this metric
calculateMetric A function that modifies the values of the
two profiles and the threshold. The new values (profile1, profile2,
threshold) are passed as arguments.
Astrid Deschenes
MetricFactory for using a interface to calculate all
available metrics separately or togheter.
It returns a list containing information about both ChIP-Seq
profiles and a list of all similarity metrics: the ratio of the
maximum values, the ratio of the areas, the ratio between the intersection
area and the total area (for normalized and non-normalized profiles), the
difference between two profiles maximal peaks positions and the Spearman's
rho statistic.
similarity(profile1, profile2, ratioAreaThreshold = 1, ratioMaxMaxThreshold = 1, ratioIntersectThreshold = 1, ratioNormalizedIntersectThreshold = 1, diffPosMaxThresholdMinValue = 1, diffPosMaxThresholdMaxDiff = 100, diffPosMaxTolerance = 0.01, spearmanCorrSDThreashold = 1e-08)similarity(profile1, profile2, ratioAreaThreshold = 1, ratioMaxMaxThreshold = 1, ratioIntersectThreshold = 1, ratioNormalizedIntersectThreshold = 1, diffPosMaxThresholdMinValue = 1, diffPosMaxThresholdMaxDiff = 100, diffPosMaxTolerance = 0.01, spearmanCorrSDThreashold = 1e-08)
profile1 |
Vector containing the RPM values of the first ChIP-Seq profile for each position of the selected region. |
profile2 |
Vector containing the RPM values of the second ChIP-Seq profile for each position of the selected region. |
ratioAreaThreshold |
The minimum denominator accepted to calculate the ratio of the area between both profiles. The value has to be positive. Default = 1. |
ratioMaxMaxThreshold |
The minimum denominator accepted to calculate the ratio of the maximal peaks values between both profiles. The value has to be positive. Default = 1. |
ratioIntersectThreshold |
The minimum denominator accepted to calculate the ratio of the intersection area of both profiles over the total area. The value has to be positive. Default = 1. |
ratioNormalizedIntersectThreshold |
The minimum denominator accepted to calculate the ratio of the intersection area of both normalized profiles over the total area. The value has to be positive. Default = 1. |
diffPosMaxThresholdMinValue |
The minimum peak accepted to calculate the metric. The value has to be positive. Default = 1. |
diffPosMaxThresholdMaxDiff |
The maximum distance accepted between 2 peaks positions in one profile to calculate the metric. The value has to be positive. Default=100. |
diffPosMaxTolerance |
The maximum of variation accepted on the maximum value to consider a position as a peak position. The value can be between 0 and 1. Default=0.01. |
spearmanCorrSDThreashold |
The minimum standard deviation accepted on both profiles to calculate the metric. Default=1e-8. |
similarity uses the two vectors passed as arguments to
calculate the metrics. When the metric is a ratio, it always verify
that the threshold for the denominator is respected. If the threshold
is not respected, the metric is assigned the NA value.
A list containing :
nbrPosition The number of positions included in each profile.
areaProfile1 The area of the first profile.
areaProfile2 The area of the second profile.
maxProfile1 The maximum value in the first profile.
maxProfile2 The maximum value in the second profile.
maxPositionProfile1 The list of positions of the maximum value
in the first profile.
maxPositionProfile2 The list of positions of the maximum value
in the second profile.
metrics A list with thefollowing items:
RATIO_AREA The ratio between the areas. The larger value is
always divided by the smaller value.NA if minimal threshold is not
respected.
DIFF_POS_MAX The difference between the maximal peaks
positions. The difference is always the first profile value minus the
second profile value. NA is returned if minimal peak value is not
respected. A profile can have more than one position with the maximum
value. In that case, the median position is used. A threshold argument
can be set to consider all positions within a certain range of the maximum
value. A threshold argument can also be set to ensure that the distance
between two maximum values is not too wide. When this distance is not
respected, it is assumed that more than one peak is present in the profile
and NA is returned.
RATIO_MAX_MAX The ratio between the maximal peaks values. The
first profile is always divided by the second profile. NA if minimal
threshold is not respected.
RATIO_INTERSECT The ratio between the intersection area and the
total area. NA if minimal threshold is not respected.
RATIO_NORMALIZED_INTERSECT The ratio between the intersection
area and the total area of normalized profiles. NA if minimal
threshold is not respected.
SPEARMAN_CORRELATION The Spearman's rho statistic between
profiles. NA if minimal threshold is not respected or when no
complete element pair is present between both profiles.
Astrid Deschenes, Elsa Bernatchez
MetricFactory for using a interface to calculate all
available metrics separately or togheter.
demoProfiles for more informations about ChIP-Seq
profiles present in the demoProfiles data.
## Defining two CHiP-Seq profiles profile1<-c(3,59,6,24,65,34,15,4,53,22,21,12,11) profile2<-c(15,9,46,44,9,39,27,34,34,4,3,4,2) ## Example usign default thresholds similarity(profile1, profile2) ## Example using customised thresholds similarity(profile1, profile2, ratioAreaThreshold=5, ratioMaxMaxThreshold=5, ratioIntersectThreshold=12, ratioNormalizedIntersectThreshold=2.2, diffPosMaxThresholdMinValue=2, diffPosMaxThresholdMaxDiff=130, diffPosMaxTolerance=0.03, spearmanCorrSDThreashold=1e-3) ## 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$chr2.70360770.70361098$H3K27ac, type="l", col="blue", xlab="", ylab="", ylim=c(0, 25), main="chr2:70360770-70361098") par(new=TRUE) plot(demoProfiles$chr2.70360770.70361098$H3K4me1, type="l", col="darkgreen", xlab="Position", ylab="Coverage in reads per million (RPM)", ylim=c(0, 25)) legend("topright", c("H3K27ac","H3K4me1"), cex=1.2, col=c("blue","darkgreen"), lty=1) # Calculate metrics similarity(demoProfiles$chr2.70360770.70361098$H3K4me1, demoProfiles$chr2.70360770.70361098$H3K27ac, ratioAreaThreshold=15, ratioMaxMaxThreshold=5, ratioIntersectThreshold=12, ratioNormalizedIntersectThreshold=2.2, diffPosMaxThresholdMinValue=2, diffPosMaxThresholdMaxDiff=130, diffPosMaxTolerance=0.03, spearmanCorrSDThreashold=0.1) ## You can refer to the vignette to see more examples using ChIP-Seq profiles ## extracted from the Encyclopedia of DNA Elements (ENCODE) data.## Defining two CHiP-Seq profiles profile1<-c(3,59,6,24,65,34,15,4,53,22,21,12,11) profile2<-c(15,9,46,44,9,39,27,34,34,4,3,4,2) ## Example usign default thresholds similarity(profile1, profile2) ## Example using customised thresholds similarity(profile1, profile2, ratioAreaThreshold=5, ratioMaxMaxThreshold=5, ratioIntersectThreshold=12, ratioNormalizedIntersectThreshold=2.2, diffPosMaxThresholdMinValue=2, diffPosMaxThresholdMaxDiff=130, diffPosMaxTolerance=0.03, spearmanCorrSDThreashold=1e-3) ## 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$chr2.70360770.70361098$H3K27ac, type="l", col="blue", xlab="", ylab="", ylim=c(0, 25), main="chr2:70360770-70361098") par(new=TRUE) plot(demoProfiles$chr2.70360770.70361098$H3K4me1, type="l", col="darkgreen", xlab="Position", ylab="Coverage in reads per million (RPM)", ylim=c(0, 25)) legend("topright", c("H3K27ac","H3K4me1"), cex=1.2, col=c("blue","darkgreen"), lty=1) # Calculate metrics similarity(demoProfiles$chr2.70360770.70361098$H3K4me1, demoProfiles$chr2.70360770.70361098$H3K27ac, ratioAreaThreshold=15, ratioMaxMaxThreshold=5, ratioIntersectThreshold=12, ratioNormalizedIntersectThreshold=2.2, diffPosMaxThresholdMinValue=2, diffPosMaxThresholdMaxDiff=130, diffPosMaxTolerance=0.03, spearmanCorrSDThreashold=0.1) ## You can refer to the vignette to see more examples using ChIP-Seq profiles ## extracted from the Encyclopedia of DNA Elements (ENCODE) data.
An object which is a interface to calculate the Spearman's
The SpearmanCorrelation object is needed to
calculate the ratio between
the peaks values between two profiles.
A threshold and the two profiles are set during the
SpearmanCorrelation
object creation. If different threshold or profiles are needed, the
calculateMetric function should be used,
with the new profiles and threshold passed as arguments to update those
values inside the SpearmanCorrelation object.
The threshold is the minimum standard deviation of the profile accepted to calculate a ratio.
SpearmanCorrelationSpearmanCorrelation
An object of class R6ClassGenerator of length 24.
The SpearmanCorrelation$new function returns a
SpearmanCorrelation object which contains the information about
the two profiles. It can be used, as many times
needed, to calculate the specified metric.
Create a SpearmanCorrelation object.
SpearmanCorrelation$new(profile1, profile2, threshold = 1e-8)
The threshold is the minimum standard deviation of the profile accepted to calculate a ratio. Default = 1e-8
The SpearmanCorrelation object inherites those functions:
getMetric A function that returns the value of the
calculated metric
getInfo A function that returns a description of the metric
with the metric value.
getType A function that returns the unique name associated
to this metric
calculateMetric A function that modifies the values of the
two profiles and the threshold. The new values (profile1, profile2)
are passed as arguments.
Astrid Deschenes
MetricFactory for using a interface to calculate all
available metrics separately or togheter.
Calculate and return the Spearman's rho statistic of two
profiles. If one profile has a standard deviation inferior to
the threshold, the function returns NA. When no complete element
pair are present, NA is returned.
spearmanCorrMethod(profile1, profile2, threshold = 1e-08)spearmanCorrMethod(profile1, profile2, threshold = 1e-08)
profile1 |
a |
profile2 |
a |
threshold |
a |
The calculated ratio or NA if one profile has a standard
deviation inferior to the threshold. If profiles have no complete element
pair, NA is returned.
Astrid Deschenes, Elsa Bernatchez
MetricFactory for using the recommanded interface to
calculate all available metrics separately or togheter.