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,... |
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