bigmelon-package | Write large-scale Illumina array datasets to CoreArray Genomic Data Structure (GDS) data files for efficient storage, access, and modification. |
'[.gds.class' | Bigmelon accessors |
'[.gdsn.class' | Bigmelon accessors |
.getEstimate2 | Bumphunter using bigmelon |
.sortvector | Compute the quantiles and ranks for a given gdsn.node |
app2gds | Append a MethyLumiSet object to a preexisting gds file |
backup.gdsn | Copy gds node to a backup folder within gds object |
betaqn-method | Bigmelon Quantile Normalization methods. |
betas-method | Bigmelon accessors |
bigmelon | Write large-scale Illumina array datasets to CoreArray Genomic Data Structure (GDS) data files for efficient storage, access, and modification. |
bigmelon-accessors | Bigmelon accessors |
bigPepo | tea.gds - description and validation for gds objects |
bumphunterEngine.gdsn | Bumphunter using bigmelon |
cantaloupe | Small MethyLumi 450k data sets for testing |
chainsaw | Chainsaw - modify gds file by subsetting all nodes |
colnames-method | Bigmelon accessors |
combo.gds | Combine two different gds objects together |
computebeta.gds | Dasen Quantile Normalization by storing ranks |
danen-method | Bigmelon Quantile Normalization methods. |
danen.gds | Bigmelon Quantile Normalization methods. |
danes-method | Bigmelon Quantile Normalization methods. |
danes.gds | Bigmelon Quantile Normalization methods. |
danet-method | Bigmelon Quantile Normalization methods. |
danet.gds | Bigmelon Quantile Normalization methods. |
dasen-method | Bigmelon Quantile Normalization methods. |
dasen.gds | Bigmelon Quantile Normalization methods. |
dasenrank | Dasen Quantile Normalization by storing ranks |
daten1-method | Bigmelon Quantile Normalization methods. |
daten1.gds | Bigmelon Quantile Normalization methods. |
daten2-method | Bigmelon Quantile Normalization methods. |
daten2.gds | Bigmelon Quantile Normalization methods. |
db.gdsn | Bigmelon Quantile Normalization methods. |
dfsfit.gdsn | Bigmelon Quantile Normalization methods. |
dim.gds.class | dim.gds.class S3 method returning dimensions of data represented by a gds file handle. |
dmrse-method | Functions imported from wateRmelon |
dmrse_col-method | Functions imported from wateRmelon |
dmrse_row-method | Functions imported from wateRmelon |
es2gds | Coersion method for MethyLumiSet, RGChannelSet or MethylSet to CoreArray Genomic Data Structure (GDS) data file |
estimateCellCounts.gds | Cell Proportion Estimation using bigmelon |
exprs-method | Bigmelon accessors |
fData-method | Bigmelon accessors |
finalreport2gds | Read finalreport files and convert to genomic data structure files |
fot | Bigmelon accessors |
fot-method | Bigmelon accessors |
gds2mlumi | Convert Genomic Data Structure file to Methylumiset or Methylset object. |
gds2mset | Convert Genomic Data Structure file to Methylumiset or Methylset object. |
genki-method | Functions imported from wateRmelon |
geotogds | Download data from GEO and convert it into a gdsfmt object |
getHistory-method | Bigmelon accessors |
getpheno | Download data from GEO and convert it into a gdsfmt object |
getquantiles | Cell Proportion Estimation using bigmelon |
getquantilesandranks | Compute the quantiles and ranks for a given gdsn.node |
honeydew | Small MethyLumi 450k data sets for testing |
iadd | Add data from Illumina IDAT files to a gds file. |
iadd2 | Add data from Illumina IDAT files to a gds file. |
idats2gds | Add data from Illumina IDAT files to a gds file. |
methylated-method | Bigmelon accessors |
nanes-method | Bigmelon Quantile Normalization methods. |
nanes.gds | Bigmelon Quantile Normalization methods. |
nanet-method | Bigmelon Quantile Normalization methods. |
nanet.gds | Bigmelon Quantile Normalization methods. |
nasen-method | Bigmelon Quantile Normalization methods. |
nasen.gds | Bigmelon Quantile Normalization methods. |
naten-method | Bigmelon Quantile Normalization methods. |
naten.gds | Bigmelon Quantile Normalization methods. |
pData-method | Bigmelon accessors |
pfilter,gds.class | Basic data filtering for Illumina methylation data in gds objects |
pfilter-method | Basic data filtering for Illumina methylation data in gds objects |
pfilter.gds | Basic data filtering for Illumina methylation data in gds objects |
prcomp, gds.class | Principal Component Analysis for high-dimensional data |
prcomp-method | Principal Component Analysis for high-dimensional data |
prcomp.gds | Principal Component Analysis for high-dimensional data |
prcomp.gds.class | Principal Component Analysis for high-dimensional data |
predictSex | Functions imported from wateRmelon |
predictSex-method | Functions imported from wateRmelon |
pvals-method | Bigmelon accessors |
pwod, gds.class | Probe-Wise Outlier Detection for DNA methylation data. |
pwod, gdsn.class | Probe-Wise Outlier Detection for DNA methylation data. |
pwod.gdsn | Probe-Wise Outlier Detection for DNA methylation data. |
QCmethylated | Bigmelon accessors |
QCmethylated-method | Bigmelon accessors |
QCrownames | Bigmelon accessors |
QCrownames-method | Bigmelon accessors |
QCunmethylated | Bigmelon accessors |
QCunmethylated-method | Bigmelon accessors |
qn.gdsn | Bigmelon Quantile Normalization methods. |
qual-method | Functions imported from wateRmelon |
redirect.gds | Change the location of the paths for row and column names in a gds file. |
rownames-method | Bigmelon accessors |
seabi-method | Functions imported from wateRmelon |
unmethylated-method | Bigmelon accessors |
wm-port | Functions imported from wateRmelon |