Description Usage Arguments Value Accessors Utilities Examples
Class REMProduct
is to maintain RE methylation prediction results.
REMProduct
inherits Bioconductor's RangedSummarizedExperiment
class.
1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 30 31 32 33 34 35 36 37 38 39 40 41 42 43 44 45 46 47 48 49 50 51 52 53 54 55 56 57 58 59 60 61 62 63 64 65 66 67 68 69 70 71 72 73 74 75 76 77 78 79 80 81 | REMProduct(
REtype = "Unknown",
genome = "Unknown",
platform = "Unknown",
win = "Unknown",
predictModel = "Unknown",
QCModel = "Unknown",
rempM = NULL,
rempB = NULL,
rempQC = NULL,
cpgRanges = GRanges(),
sampleInfo = DataFrame(),
REannotation = GRanges(),
RECpG = GRanges(),
regionCode = DataFrame(),
refGene = GRanges(),
varImp = DataFrame(),
REStats = DataFrame(),
GeneStats = DataFrame(),
Seed = NULL
)
rempM(object)
rempB(object)
rempQC(object)
rempAnnot(object)
rempImp(object)
rempStats(object)
remplot(object, ...)
details(object)
decodeAnnot(object, ...)
rempTrim(object, ...)
rempAggregate(object, ...)
rempCombine(object1, object2)
## S4 method for signature 'REMProduct'
rempM(object)
## S4 method for signature 'REMProduct'
rempB(object)
## S4 method for signature 'REMProduct'
rempQC(object)
## S4 method for signature 'REMProduct'
rempImp(object)
## S4 method for signature 'REMProduct'
rempAnnot(object)
## S4 method for signature 'REMProduct'
rempStats(object)
## S4 method for signature 'REMProduct'
remplot(object, type = c("individual", "overall"), ...)
## S4 method for signature 'REMProduct'
details(object)
## S4 method for signature 'REMProduct'
decodeAnnot(object, type = c("symbol", "entrez"), ncore = 1, BPPARAM = NULL)
## S4 method for signature 'REMProduct'
rempTrim(object, threshold = 1.7, missingRate = 0.2)
## S4 method for signature 'REMProduct'
rempAggregate(object, NCpG = 2, ncore = 1, BPPARAM = NULL)
## S4 method for signature 'REMProduct,REMProduct'
rempCombine(object1, object2)
|
REtype |
Type of RE ( |
genome |
Specify the build of human genome. Can be either |
platform |
Illumina methylation profiling platform ( |
win |
Flanking window size of the predicting RE-CpG. |
predictModel |
Name of the model used for prediction. |
QCModel |
Name of the model used for prediction quality evaluation. |
rempM |
Predicted methylation level in M value. |
rempB |
Predicted methylation level in beta value (optional). |
rempQC |
Prediction quality scores, which is available only when Random Forest
model is used in |
cpgRanges |
Genomic ranges of the predicting RE-CpG. |
sampleInfo |
Sample information. |
REannotation |
Annotation data for the predicting RE. |
RECpG |
Annotation data for the RE-CpG profiled by Illumina platform. |
regionCode |
Internal index code defined in |
refGene |
refSeq gene annotation data, which can be obtained by |
varImp |
Importance of the predictors. |
REStats |
RE coverage statistics, which is internally generated in |
GeneStats |
Gene coverage statistics, which is internally generated in |
Seed |
Random seed for Random Forest model for reproducible prediction results. |
object |
A |
... |
For |
object1 |
A |
object2 |
A |
type |
For |
ncore |
For |
BPPARAM |
For |
threshold |
For |
missingRate |
For |
NCpG |
For |
An object of class REMProduct
for the constructor.
rempM(object)
Return M value of the prediction.
rempB(object)
Return beta value of the prediction.
rempQC(object)
Return prediction quality scores.
rempImp(object)
Return relative importance of predictors.
rempStats(object)
Return RE and gene coverage statistics.
rempAnnot(object)
Return annotation data for the predicted RE.
remplot(object, type = c("individual", "overall"), ...)
Make a density plot of predicted methylation
(beta values) in the REMProduct
object. If type = "individual"
, density curves will be
plotted for each of the samples; If type = "overall"
, one density curve of the mean methylation level
across the samples will be plotted. Default type = "individual"
.
details(object)
Display detailed descriptive statistics of the predicion results.
decodeAnnot(object, type = c("symbol", "entrez")), ncore = NULL, BPPARAM = NULL
Decode the
RE annotation data by Gene Symbol (when type = "Symbol"
) or Entrez Gene
(when type = "Entrez"
).Default type = "Symbol"
. Annotation data are provided by
org.Hs.eg.db
.
rempTrim(object, threshold = 1.7, missingRate = 0.2)
Any predicted CpG values with
quality score < threshold (default = 1.7, specified by threshold = 1.7
) will be replaced with NA.
CpGs contain more than missingRate * 100
rate across samples will be discarded. Relavant summary statistics will be re-evaluated.
rempAggregate(object, NCpG = 2, ncore = NULL, BPPARAM = NULL)
Aggregate the predicted RE-CpG
methylation by RE using mean. To ensure the reliability of the aggregation, by default only RE with at
least 2 predicted CpG sites (specified by NCpG = 2
) will be aggregated.
rempCombine(object1, object2)
Combine two REMProduct
objects by column.
1 | showClass("REMProduct")
|
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