Man pages for ttriche/sesamizeGEO
the poor man's methylation suite (cf. `sesamizer`)

addCharacteristicsget the characteristics of a bunch of GSM entries
addTitlesget the titles of a bunch of GSM entries
byExtremalityFor array-based DNA methylation, particularly summarized...
cpgAnnoByChrDMRcate doesn't play nicely with HDF5-backed SEs, so I wrote...
eltsget elements from a consistently separated character string
fexpitHelper function: expanded expit
firstPassplot heatmap, remind user to check SNPs
fixNAsidiotically simple masking and imputation for sesamized...
flogitHelper function: squeezed logit
getBarcodesretrieve all the IDAT Basenames in a directory
getDMRsuse DMRcate to get DMRs (with less hassle)
getGSMsfetch supplemental data (IDATs) for a given dataset
getRGChannelSetassemble a suitable RGChannelSet for sesamizing
getSampshelper function to read in samples and Basename columns
getTxsconvenience fn
jetMatlab-style color palette
labelAnnotationslabel ComplexHeatmap annotations
loadAsHDF5EXPERIMENTAL harness to eventually bypass in-core processing...
mergeMethhelper function to merge grSets
mergeWithSNPshelper function to merge grSets while keeping their SNP...
plotSNPsanother oldie but goodie
print.dmrcate.outputsince I use DMRcate a lot, I wrote this to avoid borking the...
purifyBetasThe world's dumbest deconvolution function
rowExtremalitiesretrieve row-wise ratios of the actual SDs vs theoretical max...
saveAsHDF5EXPERIMENTAL harness to eventually bypass in-core processing...
sesamaskadd a mask to rowData(grSet) in a platform-appropriate way
sesamizeGEOsesamize a bunch of IDATs from GEO (or anywhere else with...
testIDATsmake sure annotations and so forth are in place before doing...
vafClustpunishingly simple VAF clustering for clonality estimation
ttriche/sesamizeGEO documentation built on May 28, 2019, 6:35 p.m.