| addCharacteristics | get the characteristics of a bunch of GSM entries |
| addTitles | get the titles of a bunch of GSM entries |
| asGCT | Dump DNA methylation values for quick and dirty IGV viewing |
| asMethBlocks | Collapse a GenomicRatioSet or similar over methylation blocks... |
| assayToBigWigs | Dump data as bigWig tracks for (e.g.) igv.js (which can't... |
| byExtremality | For array-based DNA methylation, particularly summarized... |
| collapseAt | Collapse a SummarizedExperiment-like object over a GRanges |
| control_metrics | bead array control processing/QC: get metrics from control... |
| dumpFromIDATs | read in a directory's worth of IDATs, flag controls,... |
| dumpQCfiles | dump QC (NAs, flags, XY stats) and (optionally) SNP calls and... |
| elts | get elements from a consistently separated character string |
| fexpit | Helper function: expanded expit |
| firstPass | plot heatmap, remind user to check SNPs |
| fitSexMix | simple function for plotting a mixture model for sex from XY... |
| flag_control_failures | Get control QA from an object returned by 'bactrl' or from an... |
| flogit | Helper function: squeezed logit |
| getBarcodes | retrieve all the IDAT Basenames in a directory |
| getGSMs | fetch supplemental data (IDATs) for a given dataset |
| getIDAT | convenience function; checks to see if an IDAT file was... |
| getRGChannelSet | assemble a suitable RGChannelSet for sesamizing |
| getSamps | helper function to read in samples and Basename columns |
| jet | Matlab-style color palette |
| labelAnnotations | label ComplexHeatmap annotations |
| merge_metadata | convenience function for merging large... |
| mergeMeth | helper function to merge grSets |
| merge_rgSets | convenience function for merging large RGChannelSets |
| mergeWithSNPs | helper function to merge grSets while keeping their SNP... |
| NAfrac | compute the fraction of sample-specific (not masked) NA... |
| plotFlaggedControls | simple function for plotting control probe failure flaggings |
| plotSNPcalls | call and plot SNPs from a matrix of SNP betas |
| plotSNPs | another oldie but goodie |
| plotXYstats | simple function for plotting XY stats (split by inferred sex... |
| processFromIDATs | read in a directory's worth of IDATs, QC them, optionally... |
| processResult | sesamize a result with sensible QC and passing BPPARAM, etc. |
| purify | The world's dumbest deconvolution function |
| regressFactors | run (e.g.) eBayes(lmFit(assay(x), design)) on columns of... |
| rename_meta | convenience function to rename columns of *Set metadata... |
| rowDataToBigWig | convenience function to dump (e.g.) W matrix values to bigWig... |
| rowExtremalities | retrieve row-wise ratios of the actual SDs vs theoretical max... |
| sesamask | add a mask to rowData(grSet) in a platform-appropriate way |
| sesamiser | like getGEO, if getGEO worked directly on IDATs and masked... |
| sesamize | "fix" a SummarizedExperiment (for which IDATs may be... |
| SNPcalls | fit a 1-to-3-component mixture model to flogit(SNPbetas) for... |
| switchMethBlocksGenome | Given an object with methylation block coordinates, switch... |
| testIDATs | make sure annotations and so forth are in place before doing... |
| vafClust | punishingly simple VAF clustering for clonality estimation |
| XYstats | compute assorted sex chromosome related statistics (XNA, YNA,... |
