Package index • PRIME

All functions

DMadjustedCV(): Calculate the distance to the median (DM) adjusted CV2 for a given RangedSummarizedExperiment object. Inspired by the method outlined in Kolodziejczyk et al., 2015, Cell Stem Cell.
TPMnormalizeBySizeFactors(): TPM normalize expression counts, considering size factors.
calcAnnoCTSS(): Calculate the total tags for each annotation type.
calcBatchSupport(): Calculate batch support for expression data.
calcCTSSComplexity(): Calculate the CTSS complexity of a CTSS dataset.
calcComplexity(): Calculate the gene and CTSS complexity of a CTSS dataset.
calcDivergentLociComplexity(): Calculate the divergent loci complexity of a CTSS dataset.
calcGeneComplexity(): Calculate the gene complexity of a CTSS dataset.
conditionalNormalize(): Conditional normalization method (e.g. on GC content) based on approach described in Pickrell, et al, 2010, Nature.
corrProfiles(): Calculate the auto correlation of CTSSs over tag clusters according to pooled values and the cross correlation with opposite strand CTSSs
corr_decompose(): Decompose tag cluster into subclusters according to CTSS expression correlation across samples.
cumulativeFractionAroundLoci(): Calculate the cumulative fraction of CTSSs around loci.
cumulativeFractionsAroundLoci(): Calculate the cumulative fraction of CTSSs around loci, considering unique tags and the fraction of loci with CTSSs.
decompose(): Decompose tag clusters according to pooled values and a decomposition function (implemented functions: summit_decompose and local_maxima_decompose)
decomposeCorr(): Decompose tag clusters according to CTSS correlations across samples
divergentLoci(): Identify divergent loci from tag clusters.
divergentLociSummit(): Identify divergent loci from tag clusters with summit centering.
divergentLociTCsSummit(): Identify divergent loci from tag clusters with summit centering. The function is similar to divergentLociSummit but does not require tag clusters to be passed to the function. This is handeled internally by calling CAGEfightR::clusterUnidirectionally on the pooled CTSS signal.
estimateDivergentNoise(): Estimate divergent loci noise in a given CTSS dataset by sampling and quantifying regions of a fixed size across the genome.
estimateNoise(): Estimate tag cluster noise in a given CTSS dataset by sampling and quantifying regions of a fixed size across the genome.
fillGaps(): Fill in missing scores across samples with zeros. Internal function used by readRange.
fingerPrint(): Calculate the complexity of a CTSS dataset and generate data for a fingerprint plot.
heatmapData(): Extract heatmap-like CTSS data for regions of fixed width with optional sparse matrix output.
initiatorScore(): Initiator classification of GRanges into YR, YC and other.
local_maxima_decompose(): Decompose tag cluster into subclusters according to CTSS expression fraction of local maxima CTSS expression. Performs local summit decomposition for each local maxima separately in decreasing order of expression level. For each local summit decomposition, subclusters will be merged if within maxGap distance. If smoothPad>0, neighbouring non-zero CTSSs within smoothPad distance of CTSSs fulfilling the summit fraction criterion will also be included. Final subclusters within mergeDist bp will be merged.
nonzero(): nonzero function from DAPAR package (https://github.com/edyp-lab/DAPAR) temporarily including a local version to avoid installation issues
normalizeBySizeFactors(): Normalize expression counts by size factors.
plotTracks(): Plot tracks for a specified genomic range using ggplot2.
poolReplicates(): Pools expression signal across replicates
quantifyClustersOlap(): Quantify the expression of disjoint tag clusters.
quantifyDivergentLoci(): Quantify the expression of divergent loci (identified by divergentLoci).
quantifyStrandwiseDivergentLoci(): import BiocGenerics
readRange(): Read bigWig files for a specified genomic range and return a tibble of scores.
rmSingletons(): Remove singleton counts from a SummarizedExperiment object. Singleton counts are those that have a value of 1 in the specified assay. This function replaces those values with 0 and stores the modified assay in a new column.
subsampleProportion(): Subsample a SummarizedExperiment to a proportion of its sequencing depth. Useful for saturation analyses.
subsampleTarget(): Subsample a SummarizedExperiment to a target sequencing depth.
summit_decompose(): Decompose tag cluster into subclusters according to CTSS expression fraction of summit CTSS expression. Subclusters within mergeDist bp will be merged.
vectorListToMatrix(): Helper function, export for PRIME model Converts a list of sparse vectors to a sparse matrix.
writeBw(): Export bigWig files for each replicate, optionally merging strands.