Bumphunter output

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WebAug 23, 2024 · The text was updated successfully, but these errors were encountered: WebHostname OS Arch (*) R version Installed pkgs; kunpeng1: Linux (Ubuntu 22.04.1 LTS) aarch64: R Under development (unstable) (2024-01-14 r83615) -- "Unsuffered Consequences"

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WebMar 13, 2015 · Output >library('GenomicRanges') Loadingrequiredpackage:BiocGenericsLoadingrequiredpackage:parallelAttachingpackage:‘BiocGenerics’ … WebThe output is an indexing variable telling us which cluster each location belongs to. Locations on different chromosomes are always on different clusters. Note that data from the ﬁrst chromosome has been split into two clusters: 3 mariah shones carlyle

Bioconductor - bumphunter

WebExample report using bumphunter results Leonardo Collado-Torres Lieber Institute for Brain Development, Johns Hopkins Medical CampusCenter for Computational Biology, Johns Hopkins University ... , "Cluster Length" = "clusterL"), significantVar = NULL, output = "bumphunter-example", outdir = "bumphunter-example", device = "png") WebIt is a collection of probes where the between probe distance (on the genome) is smaller than X. If X is set to be Inf, each chromosome will be a cluster. A region is (always) a … natural food only pet

Example report using bumphunter results • regionReport

annotateTranscripts: Annotate transcripts in bumphunter: …

WebApr 28, 2016 · The actual output of the example is below: > library(' bumphunter ') Loading required package: S4Vectors Loading required package: stats4 Loading required package: BiocGenerics Loading required package: parallel Attaching package: ... WebBut it is important to > understand that the output is merely candidate regions and (if you do > permutation testing) each region should have some associated measure > of … natural food midland txWebThe output object is a GenomicRatioSet (class holding M or/and Beta values together with associated genomic coordinates). It is possible to merge the manifest object with the genomic locations by setting the option mergeManifest to TRUE. GRset <- mapToGenome(RSet) GRset natural food opiniones

"WebNov 8, 2024 · bumphunter: Methods for function 'bumphunter' in Package 'minfi' combineArrays: A method for combining different types of methylation arrays... " - Bumphunter output

Bumphunter output

WebREADME.md. This is the developer version of the bumphunter R/Bioconductor package. Bioconductor build/check report. WebDec 24, 2024 · BumpHunter. This is the twiki page for a ROOT implementation of the BumpHunter algorithm (see http://arxiv.org/pdf/1101.0390v2.pdf ) It is installed with …

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WebThe main output is a table of candidate regions with permutation or bootstrap-based family-wide error rates (FWER) and p-values assigned. The general idea is that for each genomic location we have a value for several individuals. We also have covariates for each individual and perform regression. Webrekado pushed a commit to branch master in repository guix. commit f4eac09653ddebbe57e16824da42aad04af35632 Author: Ricardo Wurmus Date: Wed Mar 13 ...

WebNov 8, 2024 · This Simulation Data Set contains 16 samples, all of them are actually originally from one sample but modified into DMP and DMR, also alone with some errors variance. In this 16 sample dataset, we simulated 8 samples are control and 8 sample as case, samples are marked in pd of EPICSimData object. http://leekgroup.github.io/regionReport/articles/bumphunterExample.html

WebNov 8, 2024 · bumphunter: Bumphunter; clusterMaker: Make clusters of genomic locations based on distance; dummyData: Generate dummy data for use with … WebDOI: 10.18129/B9.bioc.bumphunter Bump Hunter. Bioconductor version: Release (3.16) Tools for finding bumps in genomic data. Author: Rafael A. Irizarry [aut], Martin Aryee …

WebYou need to select regions that have a low FWER, or however you want to do. But it is important to understand that the output is merely candidate regions and (if you do …

Webclarification about bumphunter value output minfi bumphunter written 5.1 years ago by src3 • 0 0. votes. 1. reply. 414. ... bumphunter DMR methylation minfi 3.2 years ago • updated 3.1 years ago i.s.brorson • 0 6. mariah shirley actressWebNov 15, 2024 · Experimental Design:Identification of differentially methylated regions (DMR) was performed with bumphunter on "The Cancer Genome Atlas (TCGA)" dataset, and clinical utility was assessed using quantitative methylation-specific PCR assay in multiple sets of primary NSCLC and body fluids that included serum, pleural effusion, and ascites … natural food perros opiniones chileWebGenerate dummy data for use with bumphunter functions. Description This function generates a small dummy dataset representing samples from two different groups (cases … mariah short storyWebHello, I am using the function matchGenes of the package bumphunter to associate many regions of interest with transcripts. I use all=TRUE in order to get several results per region. When I use all=TRUE and a small amount of queries, the output indeed contains the columns 'queries' and 'Tx' which give the query index and the matching transcript. natural food patch michiganWebMay 18, 2024 · I am using bumphunter function from minfi package for patients (Healthy donors and treatments ) dataset to find DMRs. Where i design contrasts based on the … natural food only pet dogWebNov 12, 2014 · The text was updated successfully, but these errors were encountered: natural food pantry hazeldean roadWebcpgCollapse, and bumphunter bumphunter-methods Methods for function bumphunter in Package minﬁ Description Estimate regions for which a genomic proﬁle deviates from its baseline value. Originally imple-mented to detect differentially methylated genomic regions between two populations, but can be applied to any CpG-level coefﬁcient of ... natural food midland texas