Package 'MEDIPS' - Bioconductor

More documents

Recommendations

Info

28 MEDIPS.readAlignedSequences Examples library(MEDIPSData) library(BSgenome.Hsapiens.UCSC.hg19) bam.file.hESCs.Rep1.MeDIP = system.file("extdata", "hESCs.MeDIP.Rep1.chr22.bam", package="MEDIPSData") cr=MEDIPS.seqCoverage(file=bam.file.hESCs.Rep1.MeDIP, pattern="CG", BSgenome="BSgenome.Hsapiens.UCSC.hg19", chr. MEDIPS.plotSeqCoverage(seqCoverageObj=cr, main="Sequence pattern coverage", type="pie", cov.level = c(0,1,2,3,4,5 MEDIPS.readAlignedSequences Creates a MEDIPS SET by reading a suitable input file Description Usage This function has been deprecated. Please see MEDIPS.createSet instead. Reads the input file and creates a MEDIPS SET. After reading the input file, the MEDIPS SET contains the information about the input regions, like the input file name, the dependent organism, the chromosomes included in the input file, the length of the included chromosomes (automatically loaded), the number of regions, and the start, stop and strand informations of the regions. All further slots, for example for the weighting parameters and normalized data are still empty and will be filled during the workflow. MEDIPS.readAlignedSequences(file = NULL, BSgenome = NULL, numrows = -1) Arguments file BSgenome numrows Path and file name of the input data The reference genome name as defined by BSgenome The number of short reads (number of rows) within the input file Value An object of class MEDIPSset is returned where the region dependent informations are stored in the according slots. These are informations about the input file, the reference genome, the total number of provided regions, the chromosomes which are covered by the regions, the total chromosome lengths, and the start and stop positions and strand informations of the regions. Author(s) Lukas Chavez
MEDIPS.saturation 29 Examples print("This function has been deprecated. Please see MEDIPS.createSet instead.") MEDIPS.saturation Function calculates the saturation/reproducibility of the provided IP- Seq data. Description Usage The saturation analysis addresses the question, whether the number of short reads is sufficient to generate a saturated and reproducible coverage profile of the reference genome. The main idea is that an insufficent number of short reads will not result in a saturated methylation profile. Only if there is a sufficient number of short reads, the resulting genome wide coverage profile will be reproducible by another independent set of a similar number of short reads. MEDIPS.saturation(file=NULL, BSgenome=NULL, nit=10, nrit=1, empty_bins=TRUE, rank=FALSE, extend=0, shi Arguments file BSgenome nit nrit empty_bins rank Path and file name of the IP data The reference genome name as defined by BSgenome defines the number of subsets created from the full sets of available regions (default=10) methods which randomly select data entries may be processed several times in order to obtain more stable results. By specifying the nrit parameter (default=1) it is possible to run the saturation analysis several times. The final results returned to the saturation results object are the averaged results of each random iteration step. can be either TRUE or FALSE (default TRUE). This parameter effects the way of calculating correlations between the resulting genome vectors. A genome vector consists of concatenated vectors for each included chromosome. The size of the vectors is defined by the bin_size parameter. If there occur genomic bins which contain no overlapping regions, neither from the subsets of A nor from the subsets of B, these bins will be neglected when the paramter is set to FALSE. can be either TRUE or FALSE (default FALSE). This parameter also effects the way of calculating correlations between the resulting genome vectors. If rank is set to TRUE, the correlation will be calculated for the ranks of the windows instead of considering the counts (Spearman correlation). Setting this parameter to TRUE is a more robust approach that reduces the effect of possible occuring outliers (these are windows with a very high number of overlapping regions) to the correlation.
Page 1 and 2: Package ‘MEDIPS’ May 22, 2014 T
Page 3 and 4: COUPLINGset-class 3 Details Package
Page 5 and 6: MEDIPS.annotate 5 Arguments ISet1 I
Page 7 and 8: MEDIPS.couplingVector 7 Examples li
Page 9 and 10: MEDIPS.CpGenrich 9 Examples print("
Page 11 and 12: MEDIPS.createSet 11 Arguments file
Page 13 and 14: MEDIPS.exportWIG 13 MEDIPS.exportWI
Page 15 and 16: MEDIPS.getAnnotation 15 MEDIPS.getA
Page 17 and 18: MEDIPS.mergeSets 17 Examples region
Page 19 and 20: MEDIPS.meth 19 CNV MeDIP type minRo
Page 21 and 22: MEDIPS.methylProfiling 21 score opt
Page 23 and 24: MEDIPS.methylProfiling 23 RPM_MSets
Page 25 and 26: MEDIPS.plotCoverage 25 Usage MEDIPS
Page 27: MEDIPS.plotSeqCoverage 27 Examples
Page 31 and 32: MEDIPS.saturationAnalysis 31 MEDIPS
Page 33 and 34: MEDIPS.selectSig 33 Arguments resul
Page 35 and 36: MEDIPS.selectSignificants 35 Descri
Page 37 and 38: MEDIPS.seqCoverage 37 MEDIPS.seqCov
Page 39 and 40: MEDIPSroiSet-class 39 MEDIPSroiSet-
Page 41 and 42: MEDIPSset-class 41 Objects from the
Page 43 and 44: MEDIPSset-class 43 Examples showCla
Page 45: INDEX 45 MEDIPS.createSet, 11 MEDIP

Package 'MEDIPS' - Bioconductor

Create successful ePaper yourself

Delete template?

Save as template?