Man pages for biobenkj/compartmap
Higher-order chromatin domain inference in single samples from methylation arrays and single cells from scRNA-seq and scATAC-seq

agrestiCoullCIAgresti-Coull confidence interval for a binomial proportion
array.data.chr14Example Illumina 450k methylation array data for compartmap
bootstrapCompartmentsNon-parametric bootstrapping of compartments and...
checkAssayTypeCheck if the assay is a SummarizedExperiment
cleanAssayColsRemove columns/cells/samples with NAs exceeding a threshold
cleanAssayRowsRemove rows with NAs exceeding a threshold
condenseRECondense a RaggedExperiment to a list of...
condenseSECondense the output of condenseRE to reconstruct per-sample...
dot-n_approxn_tilde in AC
dot-p_approxp_tilde in AC
dot-zNormal alpha/2 quantile
estRMTDenoising of Covariance matrix using Random Matrix Theory
extractOpenClosedGet the open and closed compartment calls based on sign of...
fexpitHelper function: expanded expit
filterCompartmentsFilter compartments using confidence estimates and eigenvalue...
filterOpenSeaFilter to open sea CpG loci
fisherZFisher's Z transformation
fixCompartmentsInvert, or "fix", compartments that have a minimum confidence...
flogitHelper function: squeezed logit
getABSignalCalculate Pearson correlations of smoothed eigenvectors
getArrayABsignalEstimate A/B compartments from methylation array data
getAssayNamesGet the assay names from a SummarizedExperiment object
getATACABsignalEstimate A/B compartments from ATAC-seq data
getBinMatrixGenerate bins for A/B compartment estimation
getChrsGet the chromosomes from an object
getCorMatrixCalculate Pearson correlations of a binned matrix
getDenoisedMatrixWrapper to denoise a correlation matrix using a Random Matrix...
getDomainInflectionsA wrapper function to generate a GRanges object of chromatin...
getGlobalMeansGet the global means of a matrix
getMatrixBlocksGet chunked sets of row-wise or column-wise indices of a...
getSeqLengthsGet the seqlengths of a chromosome
getShrinkageTargetsGet the specified samples to shrink towards instead of the...
getSVDCompute the SVD of a matrix using irlba
hdf5TFIDFTransform/normalize compartment calls using TF-IDF on...
hg19.grhg19 seqlengths as a GRanges object
hg38.grhg38 seqlengths as a GRanges object
ifisherZFisher's Z transformation
importBigWigImport and optionally summarize a bigwig at a given...
imputeKNNImpute missing values/NAs with KNN
k562_scatac_chr14Example scATAC-seq data for compartmap
k562_scrna_chr14Example scRNA-seq data for compartmap
k562_scrna_se_chr14Example scRNA-seq data for compartmap
meanSmootherWindowed mean smoother
mm10.grmm10 seqlengths as a GRanges object
mm9.grmm9 seqlengths as a GRanges object
openSeas.hg19hg19 open sea CpG as a GRanges object
openSeas.hg38hg38 open sea CpG as a GRanges object
openSeas.mm10mm10 open sea CpG as a GRanges object
openSeas.mm9mm9 open sea CpG as a GRanges object
plotABPlots A/B compartment estimates on a per chromosome basis
plotCorMatrixPlot a denoised correlation matrix
precomputeBootstrapMeansPre-compute the global means for bootstrapping compartments
preprocessArraysPreprocess arrays for compartment inference
removeEmptyBootsRemove bootstrap estimates that failed
scCompartmentsEstimate A/B compartments from single-cell sequencing data
shrinkBinsEmploy an eBayes shrinkage approach for bin-level estimates...
sparseToDenseMatrixConvert a sparse matrix to a dense matrix in a block-wise...
ss3_umi_sceExample SMART-seq3 scRNA-seq data for compartmap
summarizeBootstrapsSummarize the bootstrap compartment estimates and compute...
transformTFIDFTransform/normalize compartment calls using TF-IDF
biobenkj/compartmap documentation built on Oct. 18, 2023, 11:11 a.m.