Replication Data for: "ramr: an R package for detection of rare aberrantly methylated regions" (doi:10.18710/ED8HSD)

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Part 1: Document Description
Part 2: Study Description
Part 3: Data Files Description
Part 4: Variable Description
Part 5: Other Study-Related Materials
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Replication Data for: "ramr: an R package for detection of rare aberrantly methylated regions"

doi:10.18710/ED8HSD

DataverseNO

2020-11-30

2

Nikolaienko, Oleksii, 2020, "Replication Data for: "ramr: an R package for detection of rare aberrantly methylated regions"", https://doi.org/10.18710/ED8HSD, DataverseNO, V2, UNF:6:mHk2VYyjhtEzz5muuhFrqw== [fileUNF]

Replication Data for: "ramr: an R package for detection of rare aberrantly methylated regions"

doi:10.18710/ED8HSD

Nikolaienko, Oleksii (University of Bergen)

University of Bergen

R

comb-p

ramr

DataverseNO

University of Bergen

Nikolaienko, Oleksii

Nikolaienko, Oleksii

2020-11-24

https://doi.org/10.18710/ED8HSD

Computer and Information Science, Medicine, Health and Life Sciences, ramr, DNA methylation, Computational Biology, Epigenomics

<p>This data set contains all the necessary data sets (biologically-relevant simulated data sets, preprocessed public data sets) used to evaluate performance and obtain results using <i>ramr</i> (<a href="https://github.com/BBCG/ramr">https://github.com/BBCG/ramr</a>, <a href="http://www.bioconductor.org/packages/ramr/">http://www.bioconductor.org/packages/ramr/</a>) - a new method for identification of aberrantly methylated regions (AMRs). All the necessary R scripts that were used for preparation, testing and analysis of data sets are also provided. For additional information please check <i>ramr</i> package README.md file, vignettes or reference citation.</p> <p></p><p><b>Please use TREE VIEW to browse files efficiently</b></p>

<p></p><p><b>Abstract</b></p> <p>With recent advances in the field of epigenetics, the focus is widening from large and frequent disease- or phenotype-related methylation signatures to rare alterations transmitted mitotically or transgenerationally (constitutional epimutations). Merging evidence indicate that such constitutional alterations, albeit occurring at a low mosaic level, may confer risk of disease later in life. Given their inherently low incidence rate and mosaic nature, there is a need for bioinformatic tools specifically designed to analyse such events.</p> <p>We have developed a method (<i>ramr</i>) to identify aberrantly methylated DNA regions (AMRs). <i>ramr</i> can be applied to methylation data obtained by array or next-generation sequencing techniques to discover AMRs being associated with elevated risk of cancer as well as other diseases. We assessed accuracy and performance metrics of <i>ramr</i> and confirmed its applicability for analysis of large public data sets. Using <i>ramr</i> we identified aberrantly methylated regions that are known or may potentially be associated with development of colorectal cancer and provided functional annotation of AMRs that arise at early developmental stages.</p>

program source code

machine-readable data

machine-readable text

<a href="http://www.bioconductor.org/packages/devel/bioc/src/contrib/ramr_1.1.2.tar.gz"><i>ramr</i> package code, version 1.1.2</a>

<a href="https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE105018">GSE105018</a>: Whole blood DNA methylation profiles in participants of the Environmental Risk (E-Risk) Longitudinal Twin Study at age 18.

<a href="https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE51032">GSE51032</a>: This Series contains data from 845 participants (188 men and 657 women) in the EPIC-Italy cohort that was produced at the Human Genetics Foundation (HuGeF) in Turin, Italy.

<a href="https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE98149">GSE98149</a>: Reprogramming of H3K9me3-dependent heterochromatin during mammalian early embryo development [ChIP-seq].

<a href="https://portal.gdc.cancer.gov/projects/TCGA-COAD">TCGA-COAD</a>: The Cancer Genome Atlas Colon Adenocarcinoma data.

<p>Oleksii Nikolaienko, Per Eystein Lønning, Stian Knappskog, <i>ramr</i>: an R/Bioconductor package for detection of rare aberrantly methylated regions, Bioinformatics, 2021;, btab586</p>

10.1093/bioinformatics/btab586

<p>Oleksii Nikolaienko, Per Eystein Lønning, Stian Knappskog, <i>ramr</i>: an R/Bioconductor package for detection of rare aberrantly methylated regions, Bioinformatics, 2021;, btab586</p>

<p><i>ramr</i>: an R package for detection of rare aberrantly methylated regions. Oleksii Nikolaienko, Per Eystein Lønning, Stian Knappskog. bioRxiv 2020.12.01.403501</p>

10.1101/2020.12.01.403501

<p><i>ramr</i>: an R package for detection of rare aberrantly methylated regions. Oleksii Nikolaienko, Per Eystein Lønning, Stian Knappskog. bioRxiv 2020.12.01.403501</p>

https://github.com/BBCG/ramr

http://www.bioconductor.org/packages/ramr/

• Number of cases: 280

• No. of variables per record: 27

• Type of File: text/tab-separated-values

UNF:6:Jb8LIc18+DBR9OX2xWFcXQ==

• Number of cases: 450

• No. of variables per record: 34

• Type of File: text/tab-separated-values

UNF:6:v552E9gD4TbKA1rHJX8rRg==

• lib - lib
• delta - delta
• cutoff - cutoff
• user.self - user.self
• sys.self - sys.self
• elapsed - elapsed
• user.child - user.child
• sys.child - sys.child
• uGTP - uGTP
• uTP - uTP
• nGTP - nGTP
• nTP - nTP
• tFP - tFP
• tGTN - tGTN
• uFN - uFN
• nFN - nFN
• tTN - tTN
• uPrecision - uPrecision
• uRecall - uRecall
• uMCC - uMCC
• uF1 - uF1
• uAuPR - uAuPR
• nPrecision - nPrecision
• nRecall - nRecall
• nMCC - nMCC
• nF1 - nF1
• nAuPR - nAuPR
• lib - lib
• delta - delta
• cutoff - cutoff
• user.self - user.self
• sys.self - sys.self
• elapsed - elapsed
• user.child - user.child
• sys.child - sys.child
• uGTP - uGTP
• uTP - uTP
• nGTP - nGTP
• nTP - nTP
• tFP - tFP
• utpCor - utpCor
• ntpCor - ntpCor
• ufnCor - ufnCor
• nfnCor - nfnCor
• tGTN - tGTN
• uFN - uFN
• nFN - nFN
• tTN - tTN
• tFPR - tFPR
• uPrecision - uPrecision
• uRecall - uRecall
• uMCC - uMCC
• uF1 - uF1
• uAuROC - uAuROC
• uAuPR - uAuPR
• nPrecision - nPrecision
• nRecall - nRecall
• nMCC - nMCC
• nF1 - nF1
• nAuROC - nAuROC
• nAuPR - nAuPR

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Summary Statistics: Mean 2.9658321428571526; Max. 6.52399999999989; Min. 0.0529999999998836; StDev 2.574685161607194; Valid 280.0

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Variable Format: numeric

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Summary Statistics: StDev 1047.432738657964; Min. 11.1909999999916; Mean 530.1005142857147; Valid 280.0; Max. 3106.84100000001

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Notes: UNF:6:RrHCvfFa5ULxyPF+2LrSQg==

f86831 Location:

Summary Statistics: Valid 280.0; Min. 17.2370000000228; StDev 6075.886427847371; Max. 18043.958; Mean 2984.9033607142856

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Summary Statistics: Max. 1000.0; Min. 1000.0; Mean 1000.0; Valid 280.0; StDev 0.0

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Summary Statistics: Mean 3000.0; StDev 0.0; Max. 3000.0; Min. 3000.0; Valid 280.0

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Summary Statistics: StDev 1283.7860811085825; Min. 0.0; Max. 3000.0; Mean 1089.3785714285725; Valid 280.0

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Summary Statistics: StDev 430.14905963498774; Min. 0.0; Max. 1000.0; Valid 280.0; Mean 519.1107142857142;

Variable Format: numeric

Notes: UNF:6:5u2a7aAqSqm6ByE8nZvLqw==

f86831 Location:

Summary Statistics: Valid 280.0; Min. 0.0; StDev 1283.7860811085825; Mean 1910.6214285714275; Max. 3000.0

Variable Format: numeric

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Summary Statistics: StDev 34430.581335007344; Min. 2525539.0; Mean 2798468.2892857143; Max. 2803900.0; Valid 280.0

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Notes: UNF:6:7dsHgI7Ihd7h8iT2tjrUqQ==

f86831 Location:

Summary Statistics: StDev 0.29176290693033896; Mean 0.8762258065965057; Valid 206.0; Max. 1.0; Min. 0.00230462645696836;

Variable Format: numeric

Notes: UNF:6:4d343l2fbtqHjYYE+PUf7Q==

f86831 Location:

Summary Statistics: Mean 0.48088928571428574; Min. 0.0; Valid 280.0; StDev 0.43014905963498784; Max. 1.0;

Variable Format: numeric

Notes: UNF:6:A0ipQD/XwoESLXNOtjeQYg==

f86831 Location:

Summary Statistics: Min. 0.0316171446756817; StDev 0.3440529055838176; Max. 1.0; Mean 0.6675345244490059; Valid 206.0

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Notes: UNF:6:sQXPtSTXQ2ui2bDvNBZh8g==

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Summary Statistics: Min. 0.001998001998002; Valid 206.0; StDev 0.38176610531446126; Mean 0.6291200747058197; Max. 1.0

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Notes: UNF:6:xZvQberW2BzuCR2Mu4nYcQ==

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Summary Statistics: Min. 0.306852819440055; StDev 0.20698472463768908; Valid 216.0; Mean 0.858489891044851; Max. 1.0

Variable Format: numeric

Notes: UNF:6:7nxwuPhDw80Exua09VZfeA==

f86831 Location:

Summary Statistics: Valid 193.0; StDev 0.2677379902580225; Max. 1.0; Mean 0.8931108352547239; Min. 0.00680065794403194;

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Notes: UNF:6:36jzLiS17SYr83r9338s7g==

f86831 Location:

Summary Statistics: Min. 0.0; Mean 0.3631261904761904; Max. 1.0; StDev 0.4279286937028607; Valid 280.0;

Variable Format: numeric

Notes: UNF:6:6ct80NKBBFKQR3wH21XwEQ==

f86831 Location:

Summary Statistics: Max. 0.999666254565577; StDev 0.3887618186733151; Min. 0.0182476625090128; Mean 0.5454749370737823; Valid 193.0

Variable Format: numeric

Notes: UNF:6:bWPHnk6GDc7PzD7rIEa1sw==

f86831 Location:

Summary Statistics: Max. 0.999666555518506; Mean 0.5037172322214419; Min. 6.66444518493835E-4; Valid 193.0; StDev 0.41780202819100243

Variable Format: numeric

Notes: UNF:6:/At7hbq/QTBfGod+prBm1g==

f86831 Location:

Summary Statistics: Mean 0.9080552621673479; StDev 0.16892816465037097; Min. 0.307513762754091; Valid 232.0; Max. 1.0

Variable Format: numeric

Notes: UNF:6:VqtyknMbaKxychU+nnvSbA==

f101253 Location:

Variable Format: character

Notes: UNF:6:hjY5jxt1uv7sys6V0Q3TGA==

f101253 Location:

Summary Statistics: Mean 0.18500000000000003; Min. 0.025; Max. 0.5; Valid 450.0; StDev 0.1759795999515545

Variable Format: numeric

Notes: UNF:6:TjfPMCD0J/2fvI1pqXuYTg==

f101253 Location:

Summary Statistics: Valid 450.0; StDev 0.014941601166722848; Max. 0.05; Min. 1.0E-10; Mean 0.006111111109999996;

Variable Format: numeric

Notes: UNF:6:0b4oBfezYJIwQhbDmvWhHA==

f101253 Location:

Summary Statistics: Valid 450.0; Max. 2.02100000000002; Mean 0.3533800000000004; Min. 0.0; StDev 0.4742481237657386;

Variable Format: numeric

Notes: UNF:6:uAwbpTkoGXTEaOd0uJVoBQ==

f101253 Location:

Summary Statistics: Max. 1.32400000000001; Valid 450.0; Mean 0.4825511111111114; Min. 0.077; StDev 0.45849287171936626

Variable Format: numeric

Notes: UNF:6:dc/LkaCX/w34gVvnD29tYg==

f101253 Location:

Summary Statistics: Max. 4670.268; Mean 999.7191622222223; Valid 450.0; StDev 1555.294549330697; Min. 13.2889999999898

Variable Format: numeric

Notes: UNF:6:aHAmde5+VtvUhvKPXiWGjg==

f101253 Location:

Summary Statistics: Valid 450.0; Max. 15862.336; Mean 3622.7533133333322; Min. 40.1560000000172; StDev 5670.450848415524;

Variable Format: numeric

Notes: UNF:6:1JUQJtG65dT7N7LVt3hTkw==

f101253 Location:

Summary Statistics: Min. 4.31700000000274; StDev 254.64214734337807; Valid 450.0; Max. 1004.346; Mean 146.92694000000023;

Variable Format: numeric

Notes: UNF:6:8N+EwDHnp5lXe8PLBbTcww==

f101253 Location:

Summary Statistics: Mean 1000.0; Min. 1000.0; Valid 450.0; StDev 0.0; Max. 1000.0;

Variable Format: numeric

Notes: UNF:6:YcdsP1naXPjw5NXxnxZrGw==

f101253 Location:

Summary Statistics: Min. 0.0; StDev 423.20643390851114; Valid 450.0; Mean 520.1066666666668; Max. 1000.0

Variable Format: numeric

Notes: UNF:6:BJpDBl8WWM0lKsOgXKa39g==

f101253 Location:

Summary Statistics: Min. 3000.0; Max. 3000.0; Valid 450.0; Mean 3000.0; StDev 0.0

Variable Format: numeric

Notes: UNF:6:EMHmILdv87Iwx/XDBPZDZA==

f101253 Location:

Summary Statistics: Valid 450.0; Max. 3000.0; StDev 1297.3795023738842; Min. 0.0; Mean 1270.962222222221;

Variable Format: numeric

Notes: UNF:6:oxMUa2wBbvGOdo28WQiKuQ==

f101253 Location:

Summary Statistics: Valid 450.0; Min. 0.0; Max. 1278490.0; StDev 131775.8901566385; Mean 20049.884444444448

Variable Format: numeric

Notes: UNF:6:QgAz2FzlCdlEOJ/thysNDQ==

f101253 Location:

Summary Statistics: Valid 450.0; Mean 0.6304923738179067; Min. 0.0; Max. 0.942761762432433; StDev 0.4061453599480377

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f101253 Location:

Summary Statistics: Min. 0.0; Valid 450.0; Mean 0.5537685089531444; Max. 0.951390286187402; StDev 0.427732046412866

Variable Format: numeric

Notes: UNF:6:bIe+ut7rndNfZcBR2POxQw==

f101253 Location:

Summary Statistics: Valid 450.0; Mean 0.6147878885422986; Max. 0.915056039708211; StDev 0.3671852906366386; Min. 0.0;

Variable Format: numeric

Notes: UNF:6:P0EtDA0Lzu86SP+TQe+LDg==

f101253 Location:

Summary Statistics: StDev 0.32844821944307856; Min. 0.0; Max. 0.913474025766923; Valid 450.0; Mean 0.7177199472249159

Variable Format: numeric

Notes: UNF:6:YPxPCRzM6UFsIx+XMycVgQ==

f101253 Location:

Summary Statistics: Min. 2803900.0; Valid 450.0; Mean 2803900.0; Max. 2803900.0; StDev 0.0

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Summary Statistics: Valid 450.0; Min. 0.0; StDev 423.20643390851114; Max. 1000.0; Mean 479.89333333333326

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f101253 Location:

Summary Statistics: Min. 0.0; Valid 450.0; Max. 3000.0; Mean 1729.037777777779; StDev 1297.3795023738842

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Summary Statistics: Min. 1525410.0; Max. 2803900.0; StDev 131775.8901566385; Mean 2783850.1155555556; Valid 450.0

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Summary Statistics: Min. 0.0; StDev 0.04699735730826295; Mean 0.0071507130940634284; Valid 450.0; Max. 0.455968472484753

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Summary Statistics: StDev 0.4232064339085109; Min. 0.0; Max. 1.0; Valid 450.0; Mean 0.5201066666666666

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f101253 Location:

Summary Statistics: Valid 420.0; Min. 2.37988993009073E-6; Mean 0.5956017539091044; Max. 0.9999995004995; StDev 0.3719997502870138;

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f101253 Location:

Summary Statistics: Min. 0.00178015131286159; StDev 0.3693234078379187; Max. 1.0; Mean 0.7258924894350665; Valid 332.0;

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Summary Statistics: Min. 0.0; Max. 1.0; StDev 0.4324598341246284; Mean 0.4236540740740738; Valid 450.0;

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f101253 Location:

Summary Statistics: Mean 0.5350309033528038; Min. 0.00106817696753959; StDev 0.37234719708420705; Max. 0.999833196695076; Valid 332.0

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f101253 Location:

Summary Statistics: Mean 0.5008784837923426; Max. 0.999833361106482; StDev 0.3943974095935564; Valid 332.0; Min. 6.66444518493835E-4

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f101253 Location:

Summary Statistics: Valid 450.0; Mean 0.6650502678200866; StDev 0.38509225645045886; Min. 0.0; Max. 0.999999999881118;

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f101253 Location:

Summary Statistics: Max. 0.999999888925914; Min. 7.13118407368891E-6; Valid 390.0; Mean 0.6562494350127613; StDev 0.3498694711260333;

Variable Format: numeric

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Label:

00-README.txt

Text:

The README file

text/plain

Label:

GSE105018.data.Rdata

Text:

An R data file containing the following objects: 1. geo.ranges: a GRanges object containing beta values for 430802 CpGs across 1658 samples from GSE105018 Illumina HumanMethylation 450 data set (https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE105018). 2. sample.info: a list containing sample metadata for all samples in the GSE105018 data set. 3. sample.ids: a character vector of sample IDs.

application/gzip

Label:

GSE51032.data.Rdata

Text:

An R data file containing the following objects: 1. geo.ranges: a GRanges object containing beta values for 485512 CpGs across 845 samples from GSE51032 Illumina HumanMethylation 450 data set (https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE51032). This data set was used as a template to create simulated test data sets. 2. sample.info: a list containing sample metadata for all samples in the GSE51032 data set. 3. sample.ids: a character vector of sample IDs.

application/gzip

Label:

GRCh37.p13.2019.12.12.Rdata

Text:

An R data file containing GRanges object with all the gene coordinates from GRCh37 annotation.

application/gzip

Label:

GRCh38.p13.2020.08.10.Rdata

Text:

An R data file containing GRanges object with all the gene coordinates from GRCh38 annotation.

application/gzip

Label:

to.remove.RData

Text:

An R data file containing character vector with all polymorphic and non-specific Illumina HumanMethylation 450 probe IDs.

application/gzip

Label:

hg19ToMm9.over.chain

Text:

human hg19 to mouse mm9 liftover chain. Required for R/PoC.results.GSE105018.R.

application/octet-stream

Label:

mouse.embryonic.marks.tar.gz

Text:

LOLA database containing information on mouse embryonic chromatin marks. Required for R/PoC.results.GSE105018.R. Ungzip before using.

application/gzip

Label:

results-5-1000.Rdata

Text:

An R data file with all the performance metrics obtained by R/PoC.results.SIMULATED.R.

application/gzip

Label:

results-plots-5-1000.pdf

Text:

plots for performance metrics obtained by R/PoC.results.SIMULATED.R.

application/pdf

Label:

SIMULATED-5-1000-0.025.data.Rdata

Text:

An R data file containing the following objects: 1. simulated.ranges: a GRanges object containing simulated beta values for 485512 CpGs across 100 samples with aberrant methylation events introduced in some of the regions. 2. modified.regions.unique: a GRanges object containing genomic ranges and sample ID for 1000 true positive unique aberrantly methylated regions. 3. modified.regions.nonunique: a GRanges object containing genomic ranges and sample ID for 3000 true positive non-unique aberrantly methylated regions. 4. delta: delta value by which CpG beta values corresponding to particular region/sample pair in "simulated.ranges" were increased or decreased. 5. merge.window: "merge.window" parameter value to use during testing. 6. min.cpgs: "min.cpgs" parameter value to use during testing. 7. sample.ids: a character vector of sample IDs.

application/gzip

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SIMULATED-5-1000-0.050.data.Rdata

Text:

An R data file which is similar to "data∕SIMULATED/SIMULATED-5-1000-0.025.data.Rdata", but was generated using "delta=0.050"

application/gzip

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SIMULATED-5-1000-0.100.data.Rdata

Text:

An R data file which is similar to "data∕SIMULATED/SIMULATED-5-1000-0.025.data.Rdata", but was generated using "delta=0.100"

application/gzip

Label:

SIMULATED-5-1000-0.250.data.Rdata

Text:

An R data file which is similar to "data∕SIMULATED/SIMULATED-5-1000-0.025.data.Rdata", but was generated using "delta=0.250"

application/gzip

Label:

SIMULATED-5-1000-0.500.data.Rdata

Text:

An R data file which is similar to "data∕SIMULATED/SIMULATED-5-1000-0.025.data.Rdata", but was generated using "delta=0.500"

application/gzip

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writer-plots-5-1000.pdf

Text:

Methylation profiles of eight random genomic regions from the GSE51032 template data set (“GSE51032”) together with the methylation profiles of the same regions in each of five simulated test data sets obtained by changing beta values within those regions for a subset of samples (highlighted) by a particular delta (“delta=0.025”, “0.050”, “0.100”, “0.250” or “0.500”).

application/pdf

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files.2019-10-10.json

Text:

JSON file containing information on all Illumina Human Methylation 450 assay results in TCGA.

application/json

Label:

TCGA-COAD.tcga.data.Rdata

Text:

An R data file containing the following objects: 1. tcga.data: an object containing beta values for 487192 CpGs across 192 samples from TCGA-COAD Illumina HumanMethylation 450 data set (https://portal.gdc.cancer.gov/). This data set was used to find epimutations undergoing positive selection during carcinogenesys.

application/gzip

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tcga.coad.AMRs.Rdata

Text:

An R data file containing the following objects: 1. tcga.coad.ranges: GRanges object with TCGA-COAD subset of methylation beta values for adjacent and tumour tissue pairs. 2. tcga.coad.ramr.hg19: GRanges object with aberrantly methylated regions found in adjacent TCGA-COAD tissue samples.

application/gzip

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PoC.results.GSE105018.R

Text:

an R script to reproduce all findings from GSE105018 data set.

type/x-r-syntax

Label:

PoC.results.GSE51032.R

Text:

an R script to reproduce all findings from GSE51032 data set.

type/x-r-syntax

Label:

PoC.results.SIMULATED.R

Text:

an R script that evaluates method performance for ramr and other methods across all test scenarios. NB that some methods (e.g. comb-p) are slow, thus modern hardware and parallelism is advised. As comb-p uses at least four threads by default, it was forced to run in a single threaded mode by limiting "processes" parameter of multiprocessing.pool.Pool call to "1" in comb-p sorce code (cpv/_common.py).

type/x-r-syntax

Label:

PoC.results.TCGA-COAD.R

Text:

an R script that finds all aberantly methylated regions in a subset of adjacent tissue samples from TCGA-COAD.

type/x-r-syntax

Label:

PoC.writer.SIMULATED.R

Text:

an R script that generates simulated test data sets using GSE51032 as a template.

type/x-r-syntax

Label:

REVISION-SIMULATED-5-1000-0.025.data.Rdata

Text:

An R data file generated by revision/R/REVISION-performance-metrics.R and containing the following objects: 1. simulated.ranges: a GRanges object containing simulated beta values for 485512 CpGs across 100 samples with aberrant methylation events introduced in some of the regions. 2. modified.regions.unique: a GRanges object containing genomic ranges and sample ID for 1000 true positive unique aberrantly methylated regions. 3. modified.regions.nonunique: a GRanges object containing genomic ranges and sample ID for 3000 true positive non-unique aberrantly methylated regions. 4. modified.regions.noise: a GRanges object containing genomic ranges and sample ID for 1000 single-base aberrations. 5. delta: delta value by which CpG beta values corresponding to particular region/sample pair in "simulated.ranges" were increased or decreased. 6. merge.window: "merge.window" parameter value to use during testing. 7. min.cpgs: "min.cpgs" parameter value to use during testing. 8. sample.ids: a character vector of sample IDs.

application/gzip

Label:

REVISION-SIMULATED-5-1000-0.050.data.Rdata

Text:

An R data file which is similar to "revision∕data/REVISION-SIMULATED-5-1000-0.025.data.Rdata", but was generated using "delta=0.050". File was generated by revision/R/REVISION-performance-metrics.R.

application/gzip

Label:

REVISION-SIMULATED-5-1000-0.100.data.Rdata

Text:

An R data file which is similar to "revision∕data/REVISION-SIMULATED-5-1000-0.025.data.Rdata", but was generated using "delta=0.100". File was generated by revision/R/REVISION-performance-metrics.R.

application/gzip

Label:

REVISION-SIMULATED-5-1000-0.250.data.Rdata

Text:

An R data file which is similar to "revision∕data/REVISION-SIMULATED-5-1000-0.025.data.Rdata", but was generated using "delta=0.250". File was generated by revision/R/REVISION-performance-metrics.R.

application/gzip

Label:

REVISION-SIMULATED-5-1000-0.500.data.Rdata

Text:

An R data file which is similar to "revision∕data/REVISION-SIMULATED-5-1000-0.025.data.Rdata", but was generated using "delta=0.500". File was generated by revision/R/REVISION-performance-metrics.R.

application/gzip

Label:

REVISION-SIMULATED-plots-5-1000.pdf

application/pdf

Label:

REVISION-SIMULATED-results-5-1000.Rdata

Text:

An R data file with all the performance metrics obtained by revision/R/REVISION-performance-metrics.R.

application/gzip

Label:

REVISION-SIMULATED-suppl-plots-5-1000.pdf

Text:

plots for performance metrics generated by revision/R/REVISION-performance-metrics.R.

application/pdf

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REVISION-SIMULATED-suppl-table-5-1000.pdf

Text:

top results generated by revision/R/REVISION-performance-metrics.R.

application/pdf

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REVISION-SIMULATED-suppl-time-5-1000.pdf

Text:

time plot generated by revision/R/REVISION-performance-metrics.R.

application/pdf

Label:

REVISION-algorithm-diagram.R

Text:

an R script that builds ramr flowchart

type/x-r-syntax

Label:

REVISION-dataset-similarity.R

Text:

an R script that compares template and simulated data sets

type/x-r-syntax

Label:

REVISION-LOLA-bootstrap.R

Text:

an R script that checks LOLA analysis specificity

type/x-r-syntax

Label:

REVISION-performance-metrics.R

Text:

an R script that generates simulated test data sets using GSE51032 as a template and evaluates method performance for ramr and other methods across all test scenarios. NB that some methods (e.g. comb-p) are slow, thus modern hardware and parallelism is advised. As comb-p uses at least four threads by default, it was forced to run in a single threaded mode by limiting "processes" parameter of multiprocessing.pool.Pool call to "1" in comb-p sorce code (cpv/_common.py).

type/x-r-syntax

Label:

REVISION-ramr-dmrcate.R

Text:

an R script that compares ramr and DMRcate across various random seeds

type/x-r-syntax