**Package**: *similaRpeak*

**Authors**: Astrid Deschenes [cre, aut], Elsa Bernatchez [aut], Charles Joly Beauparlant [aut], Fabien Claude Lamaze [aut], Rawane Samb [aut], Pascal Belleau [aut], Arnaud Droit [aut]

**Version**: 1.6.0

**Compiled date**: 2016-10-17

**License**: Artistic-2.0

Astrid Deschenes, Elsa Bernatchez, Charles Joly Beauparlant, Fabien Claude Lamaze, Rawane Samb, Pascal Belleau and Arnaud Droit.

This package and the underlying similaRpeak code are distributed under the Artistic license 2.0. You are free to use and redistribute this software.

The **similaRpeak** package calculates metrics to estimate the level of similarity between two ChIP-Seq profiles.

The metrics are:

**RATIO_AREA**: The ratio between the profile areas. The first profile is always divided by the second profile.`NA`

is returned if minimal area threshold is not respected for at least one of the profiles.**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 peaks values in each profile. The first profile is always divided by the second profile.`NA`

if minimal peak value threshold is not respected for at least one of the profiles.**RATIO_INTERSECT**: The ratio between the intersection area and the total area of the two profiles.`NA`

if minimal area threshold is not respected for the intersection area.**RATIO_NORMALIZED_INTERSECT**: The ratio between the intersection area and the total area of two normalized profiles. The profiles are normalized by dividing them by their average value.`NA`

if minimal area threshold is not respected for the intersection area.**SPEARMAN_CORRELATION**: The Spearmanâ€™s rho statistic between profiles.

`suppressMessages(library(similaRpeak))`

ChIP-seq combines chromatin immunoprecipitation (ChIP) with massively parallel DNA sequencing to identify the binding sites of DNA-associated proteins. For a specific region, the read count of aligned sequences at each position of the region is used to generate the ChIP-Seq profile for the region.

To estimate the level of similarity between two ChIP-Seq profiles for a specific region, two `vector`

containing the profiles values, as reported in reads per million (RPM) for each position of the selected region, are needed. Both `vector`

should have the same length and should not contain any negative value.

Aligned sequences are usually stored in BAM files. As example, a slimmed BAM file (align1.bam) is selected as well as a specific region (chr1:172081530-172083529). Using BAM file and region information, represented by as a `GRanges`

object, the coverage for the specified region is extracted using specialized Bioconductor packages.

```
suppressMessages(library(GenomicAlignments))
suppressMessages(library(rtracklayer))
suppressMessages(library(Rsamtools))
bamFile01 <- system.file("extdata/align1.bam", package = "similaRpeak")
region <- GRanges(Rle(c("chr1")), IRanges(start = 172081530, end = 172083529),
strand= Rle(strand(c("*"))))
param <- ScanBamParam(which = region)
alignments01 <- readGAlignments(bamFile01, param = param)
coveragesRegion01 <- coverage(alignments01)[region]
coveragesRegion01
## RleList of length 1
## $chr1
## integer-Rle of length 2000 with 92 runs
## Lengths: 297 30 2 4 14 18 19 36 ... 21 15 35 36 65 36 307
## Values : 0 1 2 3 2 1 0 1 ... 2 1 0 1 0 2 0
```

The `coverages01`

can easily be transformed to a vector of numerical value to obtain the raw ChIP-Seq profile for the selected region.

```
coveragesRegion01 <- as.numeric(coveragesRegion01$chr1)
length(coveragesRegion01)
## [1] 2000
summary(coveragesRegion01)
## Min. 1st Qu. Median Mean 3rd Qu. Max.
## 0.000 0.000 0.000 0.907 1.000 6.000
```

To convert the raw coverage to reads per million (RPM), the total number of reads present in the BAM file is needed to assign a weight at the `coverage`

function.

```
param <- ScanBamParam(flag = scanBamFlag(isUnmappedQuery=FALSE))
count01 <- countBam(bamFile01, param = param)$records
coveragesRPMRegion01 <- coverage(alignments01, weight=1000000/count01)[region]
coveragesRPMRegion01 <- as.numeric(coveragesRPMRegion01$chr1)
length(coveragesRPMRegion01)
## [1] 2000
summary(coveragesRPMRegion01)
## Min. 1st Qu. Median Mean 3rd Qu. Max.
## 0.0 0.0 0.0 195.7 215.7 1294.0
```

The read per millions values are quite low for the `coveragesRPMRegion01`

because the original BAM file has been reduced in size to simplify the example.

Other examples are available on the worflows section of the Bioconductor website.

Finally, the metagene package , available on Bioconductor, can also be used to generate ChIP-Seq profiles. An example is available on metagene wiki.

Mathematically, a metric is considered as a function that quantifies the similarity between two objects.The function must return zero when the two objects are perfectly similar (identity of indiscernibles) and a non-negative value when are dissimilar.

The metrics present in the **similaRpeak** package do not strictly respect this standard but can all be translated to pseudometrics. A pseudometric is a function d which satisfies the axioms for a metric, except that instead of the identity of indiscernibles axiom, the metric must only return zero when it compare an object to itself.

By using the absolute value of the **DIFF_POS_MAX** metric, the definition of a pseudometric is formally respected. However, the respective position of the maximum peak of profiles is lost.

\[ |DIFF\_POS\_MAX| \]

By using the absolute value of the logarithm of the **RATIO_AREA**, **RATIO_MAX_MAX**, **RATIO_INTERSECT** and **RATIO_NORMALIZED_INTERSECT** metrics, the definition of a pseudometric is formally respected.

\[ |\log(RATIO)| \]

To ease comparison, the same ChIP-Seq profiles are used in each metric description section. Those are ChIP-Seq profiles 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).

Here is how to load the `demoProfiles`

data used in following sections. The ChIP-Seq profiles of the enhancers H3K27ac and H3K4me1 for 4 specifics regions are in reads per million (RPM).

```
data(demoProfiles)
str(demoProfiles)
## List of 4
## $ chr2.70360770.70361098 :List of 2
## ..$ H3K27ac: num [1:329] 13 12 12 11 11 11 9 9 7 7 ...
## ..$ H3K4me1: num [1:329] 6 7 7 7 7 8 8 8 8 9 ...
## $ chr3.73159773.73160145 :List of 2
## ..$ H3K27ac: num [1:373] 1 0 0 0 0 0 0 0 0 0 ...
## ..$ H3K4me1: num [1:373] 0 0 0 0 0 0 0 0 0 0 ...
## $ chr8.43092918.43093442 :List of 2
## ..$ H3K27ac: num [1:525] 82 82 81 81 80 80 79 78 78 76 ...
## ..$ H3K4me1: num [1:525] 1404 1398 1392 1383 1367 ...
## $ chr19.27739373.27739767:List of 2
## ..$ H3K27ac: num [1:395] 4 3 3 3 2 2 0 0 0 0 ...
## ..$ H3K4me1: num [1:395] 17 15 13 13 11 6 3 0 0 0 ...
```

The **RATIO_AREA** metric is the ratio between the profile areas. The first profile (`profile1`

parameter) is always divided by the second profile (`profile2`

parameter). `NA`

is returned if minimal area threshold (`ratioAreaThreshold`

parameter) is not respected for at least one of the profiles.

The **RATIO_AREA** metric can be useful to detect regions with similar coverage even if the profiles are different.

```
metrics <- similarity(demoProfiles$chr2.70360770.70361098$H3K27ac,
demoProfiles$chr2.70360770.70361098$H3K4me1)
metrics$metric$RATIO_AREA
## [1] 1.025942
metrics <- similarity(demoProfiles$chr8.43092918.43093442$H3K27ac,
demoProfiles$chr8.43092918.43093442$H3K4me1)
metrics$metric$RATIO_AREA
## [1] 0.05928535
metrics <- similarity(demoProfiles$chr3.73159773.73160145$H3K27ac,
demoProfiles$chr3.73159773.73160145$H3K4me1)
metrics$metric$RATIO_AREA
## [1] 2.228563
metrics <- similarity(demoProfiles$chr19.27739373.27739767$H3K27ac,
demoProfiles$chr19.27739373.27739767$H3K4me1)
metrics$metric$RATIO_AREA
## [1] 0.1245884
```

The **DIFF_POS_MAX** metric is the difference between the maximal peaks positions. The difference is always the first profile value (`profile1`

parameter) minus the second profile value (`profile2`

parameter). `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 (`diffPosMaxTolerance`

parameter) can be set to consider all positions within a certain range of the maximum value. A threshold (`diffPosMaxThresholdMaxDiff`

parameter) 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. Finally, a threshold (`diffPosMaxThresholdMinValue`

parameter) can be set to ensure that the maximum value is egal or superior to a minimal value. When this minimum value is not respected, it is assumed that no peak is present in the profile and `NA`

is returned.

The **DIFF_POS_MAX** metric can be useful to detect regions with shifted peaks.

```
metrics <- similarity(demoProfiles$chr2.70360770.70361098$H3K27ac,
demoProfiles$chr2.70360770.70361098$H3K4me1)
metrics$metric$DIFF_POS_MAX
## [1] -20
metrics <- similarity(demoProfiles$chr8.43092918.43093442$H3K27ac,
demoProfiles$chr8.43092918.43093442$H3K4me1)
metrics$metric$DIFF_POS_MAX
## [1] -0.5
metrics <- similarity(demoProfiles$chr3.73159773.73160145$H3K27ac,
demoProfiles$chr3.73159773.73160145$H3K4me1)
metrics$metric$DIFF_POS_MAX
## [1] 2.5
metrics <- similarity(demoProfiles$chr19.27739373.27739767$H3K27ac,
demoProfiles$chr19.27739373.27739767$H3K4me1)
metrics$metric$DIFF_POS_MAX
## [1] 2.5
```

The **RATIO_MAX_MAX** metric is the ratio between the peaks values in each profile. The first profile (`profile1`

parameter) is always divided by the second profile (`profile2`

parameter). `NA`

if minimal peak value threshold (`ratioMaxMaxThreshold`

parameter) is not respected for at least one of the profiles.

The **RATIO_MAX_MAX** metric can be useful to detect regions with peaks with similar (or dissimilar) amplitude.

```
metrics <- similarity(demoProfiles$chr2.70360770.70361098$H3K27ac,
demoProfiles$chr2.70360770.70361098$H3K4me1)
metrics$metric$RATIO_MAX_MAX
## [1] 0.952381
metrics <- similarity(demoProfiles$chr8.43092918.43093442$H3K27ac,
demoProfiles$chr8.43092918.43093442$H3K4me1)
metrics$metric$RATIO_MAX_MAX
## [1] 0.05840456
metrics <- similarity(demoProfiles$chr3.73159773.73160145$H3K27ac,
demoProfiles$chr3.73159773.73160145$H3K4me1)
metrics$metric$RATIO_MAX_MAX
## [1] 2.5
metrics <- similarity(demoProfiles$chr19.27739373.27739767$H3K27ac,
demoProfiles$chr19.27739373.27739767$H3K4me1)
metrics$metric$RATIO_MAX_MAX
## [1] 0.1210191
```

The **RATIO_INTERSECT** metric is the ratio between the intersection area and the total area of the two profiles. `NA`

if minimal area threshold (`ratioIntersectThreshold`

parameter) is not respected for the intersection area.

The **RATIO_INTERSECT** metric can be useful to detect regions with possibily similar profiles.

```
metrics <- similarity(demoProfiles$chr2.70360770.70361098$H3K27ac,
demoProfiles$chr2.70360770.70361098$H3K4me1)
metrics$metric$RATIO_INTERSECT
## [1] 0.6307208
metrics <- similarity(demoProfiles$chr8.43092918.43093442$H3K27ac,
demoProfiles$chr8.43092918.43093442$H3K4me1)
metrics$metric$RATIO_INTERSECT
## [1] 0.05926862
metrics <- similarity(demoProfiles$chr3.73159773.73160145$H3K27ac,
demoProfiles$chr3.73159773.73160145$H3K4me1)
metrics$metric$RATIO_INTERSECT
## [1] 0.4276368
metrics <- similarity(demoProfiles$chr19.27739373.27739767$H3K27ac,
demoProfiles$chr19.27739373.27739767$H3K4me1)
metrics$metric$RATIO_INTERSECT
## [1] 0.1231793
```

The **RATIO_NORMALIZED_INTERSECT** metric is the ratio between the intersection area and the total area of the two normalized profiles. The profiles are normalized by divinding them by their average value (total area of the profile divided by profile lenght). `NA`

if minimal area threshold (`ratioNormalizedIntersectThreshold`

parameter) is not respected for the intersection area.

The **RATIO_NORMALIZED_INTERSECT** metric can be useful to detect regions with possibily similar profiles even if their have different amplitude.

```
metrics <- similarity(demoProfiles$chr2.70360770.70361098$H3K27ac,
demoProfiles$chr2.70360770.70361098$H3K4me1)
metrics$metric$RATIO_NORMALIZED_INTERSECT
## [1] 0.6316846
metrics <- similarity(demoProfiles$chr8.43092918.43093442$H3K27ac,
demoProfiles$chr8.43092918.43093442$H3K4me1)
metrics$metric$RATIO_NORMALIZED_INTERSECT
## [1] 0.8914731
metrics <- similarity(demoProfiles$chr3.73159773.73160145$H3K27ac,
demoProfiles$chr3.73159773.73160145$H3K4me1)
metrics$metric$RATIO_NORMALIZED_INTERSECT
## [1] 0.7832524
metrics <- similarity(demoProfiles$chr19.27739373.27739767$H3K27ac,
demoProfiles$chr19.27739373.27739767$H3K4me1)
metrics$metric$RATIO_NORMALIZED_INTERSECT
## [1] 0.8439258
```

The **SPEARMAN_CORRELATION** metric is the Spearmanâ€™s rho statistic calculated usign the two profiles.`NA`

if minimal standard deviation (`spearmanCorrSDThreashold`

parameter) is not respected for at least one of the profiles.

The **SPEARMAN_CORRELATION** assesses how well the relationship between the two ChIP-Seq profiles can be described using a monotonic function. As the **RATIO_NORMALIZED_INTERSECT** metric, the **SPEARMAN_CORRELATION** metric can be useful to detect regions with possibily similar profiles even if their have different amplitude.

```
metrics <- similarity(demoProfiles$chr2.70360770.70361098$H3K27ac,
demoProfiles$chr2.70360770.70361098$H3K4me1)
metrics$metric$SPEARMAN_CORRELATION
## [1] 0.05945987
metrics <- similarity(demoProfiles$chr8.43092918.43093442$H3K27ac,
demoProfiles$chr8.43092918.43093442$H3K4me1)
metrics$metric$SPEARMAN_CORRELATION
## [1] 0.819497
metrics <- similarity(demoProfiles$chr3.73159773.73160145$H3K27ac,
demoProfiles$chr3.73159773.73160145$H3K4me1)
metrics$metric$SPEARMAN_CORRELATION
## [1] 0.9515006
metrics <- similarity(demoProfiles$chr19.27739373.27739767$H3K27ac,
demoProfiles$chr19.27739373.27739767$H3K4me1)
metrics$metric$SPEARMAN_CORRELATION
## [1] 0.6164638
```

Highly active enhancer regions are thought to be important for the cell fate (Andersson et al. 2014, FANTOM5 consortium, Hnisz et al. 2013). Highly active enhancers regions have been selected in GM12878 cells. Similarity of ChIP-seq profiles has been tested using 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). Accordingly with the literature, similarity between the profiles of these two histone marks has been identified.

First, the `similaRpeak`

package must be loaded.

`suppressMessages(library(similaRpeak))`

A region, chr7:61968807-61969730, shows interesting profiles for both histones. Letâ€™s load the data for this region.

```
data(chr7Profiles)
str(chr7Profiles)
## List of 1
## $ chr7.61968807.61969730:List of 2
## ..$ H3K27ac: num [1:924] 31 31 31 31 30 29 27 24 24 26 ...
## ..$ H3K4me1: num [1:924] 319 317 310 300 284 274 259 257 258 253 ...
```

H3K27ac and H3K4me1 profiles have those shapes:

The metrics are calculated using the `similarity`

function which takes as arguments the two ChIP-Seq profiles vectors and the threshold values.

```
metrics <- similarity(chr7Profiles$chr7.61968807.61969730$H3K27ac,
chr7Profiles$chr7.61968807.61969730$H3K4me1,
ratioAreaThreshold=5,
ratioMaxMaxThreshold=2,
ratioIntersectThreshold=5,
ratioNormalizedIntersectThreshold=2,
diffPosMaxThresholdMinValue=10,
diffPosMaxThresholdMaxDiff=100,
diffPosMaxTolerance=0.01)
```

The `similarity`

function returns a list which contains the general information about both ChIP-Seq profiles and a list of all calculated metrics.

```
metrics
## $nbrPosition
## [1] 924
##
## $areaProfile1
## [1] 22140
##
## $areaProfile2
## [1] 182991
##
## $maxProfile1
## [1] 77
##
## $maxProfile2
## [1] 646
##
## $maxPositionProfile1
## [1] 557
##
## $maxPositionProfile2
## [1] 657
##
## $metrics
## $metrics$RATIO_AREA
## [1] 0.1209896
##
## $metrics$DIFF_POS_MAX
## [1] -49.5
##
## $metrics$RATIO_MAX_MAX
## [1] 0.119195
##
## $metrics$RATIO_INTERSECT
## [1] 0.1208916
##
## $metrics$RATIO_NORMALIZED_INTERSECT
## [1] 0.8478406
##
## $metrics$SPEARMAN_CORRELATION
## [1] 0.9689683
```

Each specific information can be directly accessed. Some examples:

```
metrics$areaProfile1
## [1] 22140
metrics$areaProfile2
## [1] 182991
metrics$metrics$RATIO_INTERSECT
## [1] 0.1208916
```

The **RATIO_INTERSECT** value of 0.12 and the **RATIO_MAX_MAX** value of 0.12 are quite low. Both values can be explained by the large difference in coverage between profiles. Those values could be interpreted as two profiles with low level of similarity. However, the **RATIO_NORMALIZED_INTERSECT** of 0.85 is much closer to 1. It could be a sign that the profiles, once normalized, are quite similar. This hypothesis can be validated by looking at a graph of the normalized profiles :

It is possible to create only one selected metric by using the **MetricFactory** object (with the possibility of specifying the thresholds) and by passing the name of the metric to create (**RATIO_AREA**, **DIFF_POS_MAX**, **RATIO_MAX_MAX**, **RATIO_INTERSECT** or **RATIO_NORMALIZED_INTERSECT**):

`factory = MetricFactory$new(diffPosMaxTolerance=0.04)`

The factory has to be iniatized only once and can be used as many times as necessary. It can calculate the same metrics but with different profiles or different metrics with same profiles as long as the thresholds values remain the same:

```
ratio_max_max <- factory$createMetric(metricType="RATIO_MAX_MAX",
profile1=demoProfiles$chr2.70360770.70361098$H3K27ac,
profile2=demoProfiles$chr2.70360770.70361098$H3K4me1)
ratio_max_max
## $RATIO_MAX_MAX
## [1] 0.952381
ratio_normalized_intersect <- factory$createMetric(
metricType="RATIO_NORMALIZED_INTERSECT",
profile1=demoProfiles$chr2.70360770.70361098$H3K27ac,
profile2=demoProfiles$chr2.70360770.70361098$H3K4me1)
ratio_normalized_intersect
## $RATIO_NORMALIZED_INTERSECT
## [1] 0.6316846
```

Here is the output of `sessionInfo()`

on the system on which this document was compiled:

```
## R version 3.3.1 (2016-06-21)
## Platform: x86_64-pc-linux-gnu (64-bit)
## Running under: Ubuntu 16.04.1 LTS
##
## locale:
## [1] LC_CTYPE=en_US.UTF-8 LC_NUMERIC=C
## [3] LC_TIME=en_US.UTF-8 LC_COLLATE=C
## [5] LC_MONETARY=en_US.UTF-8 LC_MESSAGES=en_US.UTF-8
## [7] LC_PAPER=en_US.UTF-8 LC_NAME=C
## [9] LC_ADDRESS=C LC_TELEPHONE=C
## [11] LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C
##
## attached base packages:
## [1] stats4 parallel stats graphics grDevices utils datasets
## [8] methods base
##
## other attached packages:
## [1] rtracklayer_1.34.0 GenomicAlignments_1.10.0
## [3] Rsamtools_1.26.0 Biostrings_2.42.0
## [5] XVector_0.14.0 SummarizedExperiment_1.4.0
## [7] Biobase_2.34.0 GenomicRanges_1.26.0
## [9] GenomeInfoDb_1.10.0 IRanges_2.8.0
## [11] S4Vectors_0.12.0 BiocGenerics_0.20.0
## [13] similaRpeak_1.6.0 R6_2.2.0
## [15] knitr_1.14 BiocStyle_2.2.0
##
## loaded via a namespace (and not attached):
## [1] Rcpp_0.12.7 magrittr_1.5 zlibbioc_1.20.0
## [4] BiocParallel_1.8.0 lattice_0.20-34 stringr_1.1.0
## [7] tools_3.3.1 grid_3.3.1 htmltools_0.3.5
## [10] yaml_2.1.13 assertthat_0.1 digest_0.6.10
## [13] tibble_1.2 Matrix_1.2-7.1 formatR_1.4
## [16] bitops_1.0-6 RCurl_1.95-4.8 evaluate_0.10
## [19] rmarkdown_1.1 stringi_1.1.2 XML_3.98-1.4
```

Andersson R, Gebhard C, Miguel-Escalada I, Hoof I, Bornholdt J, et al. (2014) An atlas of active enhancers across human cell types and tissues. Nature, 507(7493), 455-461.

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.

Forrest AR, Kawaji H, Rehli M, Baillie JK, de Hoon MJ, et al. (2014) A promoter-level mammalian expression atlas. Nature, 507(7493):462-470.

Hnisz D, Abraham BJ, Lee TI, Lau A, Saint-AndrĂ© V, et al. (2013) Super-enhancers in the control of cell identity and disease. Cell, 155(4), 934-947.