genomicratioset: 'GenomicRatioSet' class object, created from...
In yocra3/epimutacions: Robust Outlier identification for DNA methylation data
Description
Usage
Format
Details
Value
Examples
Description
GenomicRatioSet object, annotated with
IlluminaHumanMethylation450kanno.ilmn12.hg19 data
with contiguous CpG choosing on 15 chr.
Usage
1
data("genomicratioset")
Format
An object of class GenomicRatioSet with 20 rows and 20 columns.
Details
Dimensions: The dataset consist of 20 rows (representing CpG islands)
and 5 columns (representing samples)
Sample choosing was done with subseting the default Locations
dataframe:
chr15 <- data.frame(Locations)
filter(chr == 'chr15')
After that, new dataframe was ordered by position in ascending order
and slice with 20 CpG names was taken:
row_n <- rownames(arrange(chr15, chr15$pos)[1178:1197,])
The difference in position between 1197 and 1178 element is
731 bp.
The geneticratioset was created via:
geneticratioset <- makeGenomicRatioSetFromMatrix(methylation_matrix,
rownames = row_n, pData = data.frame(id = c("case_1", "case_2", "case_3",
"case_4", "case_5")))
Value
A GenomicRatioSet object.
Examples
1
2
3
data("methylation_matrix")
dim(methylation_matrix)
sampleNames(genomicratioset)
yocra3/epimutacions documentation built on Jan. 1, 2021, 1:46 p.m.
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Description Usage Format Details Value Examples
Description
GenomicRatioSet object, annotated with
IlluminaHumanMethylation450kanno.ilmn12.hg19 data
with contiguous CpG choosing on 15 chr.
Usage
1 | data("genomicratioset")
|
Format
An object of class GenomicRatioSet with 20 rows and 20 columns.
Details
Dimensions: The dataset consist of 20 rows (representing CpG islands) and 5 columns (representing samples)
Sample choosing was done with subseting the default Locations
dataframe:
chr15 <- data.frame(Locations)
filter(chr == 'chr15')
After that, new dataframe was ordered by position in ascending order
and slice with 20 CpG names was taken:
row_n <- rownames(arrange(chr15, chr15$pos)[1178:1197,])
The difference in position between 1197 and 1178 element is
731 bp.
The geneticratioset was created via:
geneticratioset <- makeGenomicRatioSetFromMatrix(methylation_matrix,
rownames = row_n, pData = data.frame(id = c("case_1", "case_2", "case_3",
"case_4", "case_5")))
Value
A GenomicRatioSet object.
Examples
1 2 3 | data("methylation_matrix")
dim(methylation_matrix)
sampleNames(genomicratioset)
|
R Package Documentation
Browse R Packages
We want your feedback!
Note that we can't provide technical support on individual packages. You should contact the package authors for that.
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