beadc |
Calculates the number of samples with bead count <3 for each probe in matrix of bead count values |
beadcount |
Creates matrix of beacounts from minfi data. |
Beta2M |
Internal functions for peak.correction (fuks) |
betaqn |
Calculate normalized betas from Illumina 450K methylation arrays |
betaqn-method |
Calculate normalized betas from MethyLumiSets of Illumina 450K methylation arrays |
betaqn-method |
Calculate normalized betas from Illumina 450K methylation arrays |
betaqn-method |
Calculate normalized betas from exprmethy450 of Illumina 450K methylation arrays |
bfp |
Internal functions for readEPIC and other wateRmelon functions introduced in v 1.13.1 |
bgIntensitySwan.methylumi |
Functions from 450-pipeline (Touleimat & Tost) |
BMIQ |
Beta-Mixture Quantile (BMIQ) Normalisation method for Illumina 450k arrays |
BMIQ-method |
Beta-Mixture Quantile (BMIQ) Normalisation method for Illumina 450k arrays |
BMIQ-methods |
Beta-Mixture Quantile (BMIQ) Normalisation method for Illumina 450k arrays |
bscon |
Calculate bisulphite conversion |
bscon-method |
Calculate bisulphite conversion |
bscon_methy |
Internal functions for readEPIC and other wateRmelon functions introduced in v 1.13.1 |
bscon_minfi |
Internal functions for readEPIC and other wateRmelon functions introduced in v 1.13.1 |
CheckBMIQ |
Beta-Mixture Quantile (BMIQ) Normalisation method for Illumina 450k arrays |
coef |
Age Prediction from methylomic expression data |
colnames-method |
Methods for Function 'colnames' in Package 'wateRmelon' |
colnames-methods |
Methods for Function 'colnames' in Package 'wateRmelon' |
columnMatrix |
Internal functions for readEPIC and other wateRmelon functions introduced in v 1.13.1 |
combo |
Combine MethyLumiSet objects |
concatenateMatrices |
Functions from 450-pipeline (Touleimat & Tost) |
coRankedMatrices |
Functions from 450-pipeline (Touleimat & Tost) |
correctI |
Internal functions for peak.correction (fuks) |
correctII |
Internal functions for peak.correction (fuks) |
danen |
Calculate normalized betas from Illumina 450K methylation arrays |
danen-method |
Calculate normalized betas from MethyLumiSets of Illumina 450K methylation arrays |
danen-method |
Calculate normalized betas from Illumina 450K methylation arrays |
danes |
Calculate normalized betas from Illumina 450K methylation arrays |
danes-method |
Calculate normalized betas from MethyLumiSets of Illumina 450K methylation arrays |
danes-method |
Calculate normalized betas from Illumina 450K methylation arrays |
danet |
Calculate normalized betas from Illumina 450K methylation arrays |
danet-method |
Calculate normalized betas from MethyLumiSets of Illumina 450K methylation arrays |
danet-method |
Calculate normalized betas from Illumina 450K methylation arrays |
dasen |
Calculate normalized betas from Illumina 450K methylation arrays |
dasen-method |
Calculate normalized betas from MethyLumiSets of Illumina 450K methylation arrays |
dasen-method |
Calculate normalized betas from Illumina 450K methylation arrays |
dataDetectPval2NA |
Functions from 450-pipeline (Touleimat & Tost) |
DataToNChannelSet2 |
Internal functions for readEPIC and other wateRmelon functions introduced in v 1.13.1 |
daten1 |
Calculate normalized betas from Illumina 450K methylation arrays |
daten1-method |
Calculate normalized betas from MethyLumiSets of Illumina 450K methylation arrays |
daten1-method |
Calculate normalized betas from Illumina 450K methylation arrays |
daten2 |
Calculate normalized betas from Illumina 450K methylation arrays |
daten2-method |
Calculate normalized betas from MethyLumiSets of Illumina 450K methylation arrays |
daten2-method |
Calculate normalized betas from Illumina 450K methylation arrays |
db1 |
Internal wateRmelon functions for calculating betas |
designIItoMandU2 |
Internal functions for readEPIC and other wateRmelon functions introduced in v 1.13.1 |
designItoMandU2 |
Internal functions for readEPIC and other wateRmelon functions introduced in v 1.13.1 |
detectionPval.filter |
Functions from 450-pipeline (Touleimat & Tost) |
dfort |
Internal functions for readEPIC and other wateRmelon functions introduced in v 1.13.1 |
dfs2 |
Internal wateRmelon functions for calculating betas |
dfsfit |
Internal wateRmelon functions for calculating betas |
dmrse |
Standard error of iDMR 450k array DNA methylation features |
dmrse-method |
Methods for Function 'dmrse' in Package 'wateRmelon' |
dmrse-methods |
Methods for Function 'dmrse' in Package 'wateRmelon' |
dmrse_col |
Standard error of iDMR 450k array DNA methylation features |
dmrse_col-method |
Methods for Function 'dmrse' in Package 'wateRmelon' |
dmrse_col-methods |
Methods for Function 'dmrse' in Package 'wateRmelon' |
dmrse_row |
Standard error of iDMR 450k array DNA methylation features |
dmrse_row-method |
Methods for Function 'dmrse' in Package 'wateRmelon' |
dmrse_row-methods |
Methods for Function 'dmrse' in Package 'wateRmelon' |
gcoms |
Internal functions for genotype-based normalization metrics |
gcose |
Internal functions for genotype-based normalization metrics |
genall |
Internal functions for readEPIC and other wateRmelon functions introduced in v 1.13.1 |
generateManifest |
Internal functions for readEPIC and other wateRmelon functions introduced in v 1.13.1 |
genki |
SNP derived performance metrics for Illumina 450K DNA methylation arrays. |
genki-method |
Methods for Function 'genki' in Package 'wateRmelon' |
genki-methods |
Methods for Function 'genki' in Package 'wateRmelon' |
genkme |
Internal functions for genotype-based normalization metrics |
genkus |
Internal functions for genotype-based normalization metrics |
genme |
Internal functions for readEPIC and other wateRmelon functions introduced in v 1.13.1 |
genus |
Internal functions for readEPIC and other wateRmelon functions introduced in v 1.13.1 |
getColumns |
Methods for Function 'as.methylumi' |
getControlProbes2 |
Internal functions for readEPIC and other wateRmelon functions introduced in v 1.13.1 |
getMethylationBeadMappers2 |
Internal functions for readEPIC and other wateRmelon functions introduced in v 1.13.1 |
getMethylumiBeta |
Functions from 450-pipeline (Touleimat & Tost) |
getQuantiles |
Functions from 450-pipeline (Touleimat & Tost) |
getSamples |
Functions from 450-pipeline (Touleimat & Tost) |
getsnp |
Internal functions for genotype-based normalization metrics |
goodSNP |
Internal functions for readEPIC and other wateRmelon functions introduced in v 1.13.1 |
got |
Internal functions for Illumina i450 normalization functions |
nanes |
Calculate normalized betas from Illumina 450K methylation arrays |
nanes-method |
Calculate normalized betas from MethyLumiSets of Illumina 450K methylation arrays |
nanes-method |
Calculate normalized betas from Illumina 450K methylation arrays |
nanet |
Calculate normalized betas from Illumina 450K methylation arrays |
nanet-method |
Calculate normalized betas from MethyLumiSets of Illumina 450K methylation arrays |
nanet-method |
Calculate normalized betas from Illumina 450K methylation arrays |
nasen |
Calculate normalized betas from Illumina 450K methylation arrays |
nasen-method |
Calculate normalized betas from MethyLumiSets of Illumina 450K methylation arrays |
nasen-method |
Calculate normalized betas from Illumina 450K methylation arrays |
naten |
Calculate normalized betas from Illumina 450K methylation arrays |
naten-method |
Calculate normalized betas from MethyLumiSets of Illumina 450K methylation arrays |
naten-method |
Calculate normalized betas from Illumina 450K methylation arrays |
nbBeadsFilter |
Functions from 450-pipeline (Touleimat & Tost) |
NChannelSetToMethyLumiSet2 |
Internal functions for readEPIC and other wateRmelon functions introduced in v 1.13.1 |
normalize.quantiles2 |
Functions from 450-pipeline (Touleimat & Tost) |
normalizeIlluminaMethylation |
Functions from 450-pipeline (Touleimat & Tost) |
pcouted |
Internal functions for readEPIC and other wateRmelon functions introduced in v 1.13.1 |
pfilter |
Basic data filtering for Illumina 450 methylation data |
pfilter-method |
Basic data filtering for Illumina 450 methylation data |
pfilter-methods |
Basic data filtering for Illumina 450 methylation data |
pipelineIlluminaMethylation.batch |
Functions from 450-pipeline (Touleimat & Tost) |
plot_predicted_sex |
Internal functions for readEPIC and other wateRmelon functions introduced in v 1.13.1 |
pop |
Internal functions for Illumina i450 normalization functions |
preprocessIlluminaMethylation |
Functions from 450-pipeline (Touleimat & Tost) |
pwod |
Probe-Wise Outlier Detection |
pwod-method |
Methods for Function 'pwod' in Package 'wateRmelon' |
p_dfsfit |
Internal functions for readEPIC and other wateRmelon functions introduced in v 1.13.1 |
seabi |
Calculate a performance metric based on male-female differences for Illumina methylation 450K arrays |
seabi-method |
Methods for Function 'seabi' in Package 'wateRmelon' |
seabi-methods |
Methods for Function 'seabi' in Package 'wateRmelon' |
seabi2 |
Internal functions for readEPIC and other wateRmelon functions introduced in v 1.13.1 |
seabird |
Calculate ROC area-under-curve for X-chromosome sex differences (internal function for calculating the seabi metric) |
seabird2 |
Internal functions for readEPIC and other wateRmelon functions introduced in v 1.13.1 |
sextest |
Test Illumina methylation 450K array probes for sex difference (internal function for calculating 'seabi' performance metric) |
sex_coef |
Predict sex by using robust sex-related CpG sites on ChrX and ChrY |
sort_order |
Internal functions for readEPIC and other wateRmelon functions introduced in v 1.13.1 |
subbo |
Internal functions for readEPIC and other wateRmelon functions introduced in v 1.13.1 |
summits |
Internal functions for peak.correction (fuks) |
swan |
Calculate normalized betas from Illumina 450K methylation arrays |
swan-method |
Calculate normalized betas from MethyLumiSets of Illumina 450K methylation arrays |
swan-method |
Calculate normalized betas from Illumina 450K methylation arrays |