Description Usage Arguments Value Examples
rempTemplate
is used to build a set of data templates for prediction. The data templates include
RE-CpGs and their methylation data for model training, neighboring CpGs of RE-CpGs and their
methylation data for model prediction, and other necessary information about the prediction.
This function is useful when one needs to experiment different tunning parameters so that these pre-built
data templates can be re-used and substaintially improve efficiency.
1 2 3 4 5 6 7 | rempTemplate(
methyDat = NULL,
Seq.GR = NULL,
parcel = NULL,
win = 1000,
verbose = FALSE
)
|
methyDat |
A |
Seq.GR |
A |
parcel |
An |
win |
An integer specifying window size to confine the upstream and downstream flanking
region centered on the predicted CpG in RE for prediction. Default = |
verbose |
Logical parameter. Should the function be verbose? |
A template
object containing a GRanges
object of neifhboring CpGs of RE-CpGs
to be predicted ($NBCpG_GR
) and their methylation dataset matrix ($NBCpG_methyDat
);
a GRanges
object of RE-CpGs for model training ($RECpG_GR
) and their methylation
dataset matrix ($RECpG_methyDat
); GRanges
objects of RefSeq Gene database ($refgene
)
and RE ($RE
) that are extracted from the parcel
input; a string of RE type ($REtype
)
and a string of methylation platform ($arrayType
). Note: the subset operator []
is supported.
1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 | if (!exists("GM12878_450k"))
GM12878_450k <- getGM12878("450k")
if (!exists("remparcel")) {
data(Alu.hg19.demo)
remparcel <- initREMP(arrayType = "450k",
REtype = "Alu",
annotation.source = "AH",
genome = "hg19",
RE = Alu.hg19.demo,
ncore = 1,
verbose = TRUE)
}
template <- rempTemplate(GM12878_450k,
parcel = remparcel,
win = 1000,
verbose = TRUE)
template
## To make a subset
template[1]
|
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