This report was generated with RLSeq v0.99.3.
Sample name: SRX1070676
Sample type: DRIP
Label: POS
Genome: hg38
Time: Thu Oct 7 09:38:01 2021
Result | Available |
---|---|
RLFS Analysis | TRUE |
Sample classification | TRUE |
Feature enrichment test | TRUE |
Correlation analysis | FALSE |
Gene Annotations | TRUE |
RL-Regions Test | TRUE |
R-loop forming sequences (RLFS) were compared to the ranges in SRX1070676 to measure enrichment. The resulting Z-score distribution is visualized below:
Note: for samples which map R-loop successfully, enrichment is expected. See representative examples for POS and NEG sample types here.
RLFS were derived across the genome using QmRLFS-finder.py
. R-loop broad peaks were called with macs
and then compared with RLFS using permTest
from the regioneR
R package. An empirical distribution of RLFS was generated using the circularRandomizeRegions
method and compared to the peaks in order to calculate enrichment p value and zscore (effect size of enrichment).
From this analysis, the empirically-determined p value was 0.009901 (with 100 permutations, the minimum possible p value was 0.009901). The enrichment z-score was 37.0012.
Predicted label for sample SRX1070676 is “POS” (i.e., robust R-loop mapping).
To evaluate sample quality, a binary classifier was developed via the online-learning approach described in the RLSuite manuscript. The classifier evaluates features engineered from the RLFS Z score distribution, specifically, the following features:
feature | description | raw_value | processed_value |
---|---|---|---|
Z1 | mean of Z | 0.3115924 | 21.4719243 |
Z2 | variance of Z | 0.2000516 | 334.6593397 |
Zacf1 | mean of Z ACF | 0.0373472 | 0.2391912 |
Zacf2 | variance of Z ACF | 0.3868038 | 582.5396127 |
ReW1 | mean of FT of Z (real part) | 0.2909243 | 12.2412218 |
ReW2 | variance of FT of Z (real part) | 0.2049347 | 4744.2587764 |
ImW1 | mean of FT of Z (imaginary part) | 0.8892123 | 0.0000000 |
ImW2 | variance of FT of Z (imaginary part) | -0.7306497 | 58.1400446 |
ReWacf1 | mean of FT of Z ACF (real part) | 0.3259641 | 96.1548430 |
ReWacf2 | variance of FT of Z ACF (real part) | 0.3919846 | 6270.2386954 |
ImWacf1 | mean of FT of Z ACF (imaginary part) | -0.0883951 | 0.0000000 |
ImWacf2 | variance of FT of Z ACF (imaginary part) | 0.3647679 | 5375.3082857 |
From these features, classification was performed to derive a prediction (predicted label) regarding whether the sample mapped R-loops or not. In short, “POS” indicates any sample for which all the following are true:
The criteria for SRX1070676 are shown below:
Criteria | Result |
---|---|
|
TRUE |
|
TRUE |
|
TRUE |
|
TRUE |
These results led to the final prediction: “POS” (i.e., robust R-loop mapping).
The results were then visualized with the plotEnrichment()
function:
Note: If < 200 peaks in user-supplied sample, ◇ will be missing from plots.
Annotations were derived from a variety of sources and accessed using RLHub (unless custom annotations were supplied by the user). Detailed explanations of each database and type can be found here. The valr
R package was implemented to test the enrichment of these features within the supplied ranges for SRX1070676.
Unavailable. Run corrAnalyze()
and then report()
again to view this result.
hg38 Gene annotations were downloaded from AnnotationHub and overlapped with R-loop ranges in SRX1070676. The resulting gene table was then filtered for the top 2000 peaks (by p-adjusted value) and is observed here:
RL-Regions are consensus R-loop sites derived from a meta-analysis of all high-confidence R-loop mapping samples in RLBase (see the RLSuite manuscript for a full description). The ranges supplied for SRX1070676 were compared to the RL-Regions to determine the degree and significance of overlap.
For more information about RLSeq please visit the package homepage here.
Note: if you use RLSeq in published research, please reference:
Miller et al., RLSeq, (2021), GitHub repository, Bishop-Laboratory/RLSeq
## R version 4.1.1 (2021-08-10)
## Platform: x86_64-pc-linux-gnu (64-bit)
## Running under: Ubuntu 20.04.3 LTS
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## Matrix products: default
## BLAS: /usr/lib/x86_64-linux-gnu/blas/libblas.so.3.9.0
## LAPACK: /usr/lib/x86_64-linux-gnu/lapack/liblapack.so.3.9.0
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## [11] LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C
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## attached base packages:
## [1] stats graphics grDevices utils datasets methods base
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## other attached packages:
## [1] RLHub_0.99.4 RLSeq_0.99.3 dplyr_1.0.7 magrittr_2.0.1
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## loaded via a namespace (and not attached):
## [1] AnnotationHub_3.1.5 BiocFileCache_2.1.1
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## [119] rtracklayer_1.53.1 GenomicRanges_1.45.0
## [121] R6_2.5.1 BiocIO_1.3.0
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RLSeq © 2021, Bishop Lab, UT Health San Antonio
RLSeq maintainer: Henry Miller