Package 'sesameData'

Title: Supporting Data for SeSAMe Package
Description: Provides supporting annotation and test data for SeSAMe package. This includes chip tango addresses, mapping information, performance annotation, and trained predictor for Infinium array data. This package provides user access to essential annotation data for working with many generations of the Infinium DNA methylation array. Currently we support human array (HM27, HM450, EPIC), mouse array (MM285) and the HorvathMethylChip40 (Mammal40) array.
Authors: Wanding Zhou [aut, cre, fnd] (ORCID: <https://orcid.org/0000-0001-9126-1932>), Hui Shen [aut, fnd], Timothy Triche [ctb]
Maintainer: Wanding Zhou <[email protected]>
License: Artistic-2.0
Version: 1.31.1
Built: 2026-10-13 03:54:41 UTC
Source: https://github.com/bioc/sesameData

Help Index

build GENCODE gtf

Description

build GENCODE gtf

Usage

build_GENCODE_gtf(x)

Arguments

x

GENCODE ftp url

Value

GRangesList

Master data frame for all object to cache

Description

This is an internal object which will be updated on every new release library(ExperimentHub) eh <- query(ExperimentHub(localHub=FALSE), c("sesameData", "v1.13.1")) data.frame(name=eh$title, eh=names(eh))

Format

A data frame with 22 columns:

Comments

Additional comments

EHID

ExperimentHub ID

VERSION

sesameData version

IN_USE

Logical indicating if the resource is in use

Title

Title of the data resource

Description

Description of the data resource

BiocVersion

Bioconductor version

Genome

Genome build (e.g., hg38, mm10)

SourceType

Source file type

SourceUrl

URL to source

SourceVersion

Version of source data

Species

Species name

TaxonomyId

NCBI Taxonomy ID

Coordinate_1_based

Logical indicating if coordinates are 1-based

DataProvider

Data provider name

Maintainer

Maintainer contact information

RDataClass

R data class

DispatchClass

Dispatch class for ExperimentHub

RDataPath

Path to RData file

Location_Prefix

URL prefix for data location

Tags

Tags for categorization

Notes

Additional notes

Details

Cache location is default to /Users/zhouw3/Library/Caches/org.R-project.R/R/ExperimentHub/

Value

master sheet of sesameData objects

Extend a GRanges

Description

source: https://support.bioconductor.org/p/78652/

Usage

extend(gr, upstream = 0, downstream = 0)

Arguments

gr

a GenomicRanges::GRanges
upstream

distance to expand upstream
downstream

distance to expand downstream

Value

a GenomicRanges::GRanges

infer platform from Probe_IDs

Description

infer platform from Probe_IDs

Usage

inferPlatformFromProbeIDs(Probe_IDs, silent = FALSE)

Arguments

Probe_IDs

probe IDs
silent

suppress message

Value

a platform code

Examples

sesameDataCache("probeIDSignature")
inferPlatformFromProbeIDs(c("cg14620903","cg22464003"))

Annotate Probes by Probe ID

Description

This function annotates probes based on genomic coordinate overlaps with provided genomic regions (GRanges). Columns in the manifests will be added to the annotation. Please note that if unfound, the annotation will be NA. The probe will always be kept in the output.

Usage

sesameData_annoProbes(
  Probe_IDs,
  regs = NULL,
  collapse = TRUE,
  chooseOne = FALSE,
  column = NULL,
  sep = ",",
  return_ov_probes = FALSE,
  return_ov_features = FALSE,
  out_name = NULL,
  platform = NULL,
  genome = NULL,
  silent = FALSE
)

Arguments

Probe_IDs

a character vector of probe IDs
regs

a GenomicRanges::GRanges object against which probes will be annotated, default to genes if not given
collapse

whether to collapse multiple regs into one
chooseOne

choose an arbitrary annotation if multiple exist default to FALSE. which concatenates all with ","
column

which column in regs to annotate, if not given return all overlapping probes
sep

the delimiter for collapsing
return_ov_probes

if TRUE will return overlapping probes in a GRanges object.
return_ov_features

if TRUE will return overlapping features in a GRanges object.
out_name

column header of the annotation, use column if not given
platform

EPIC, MM285 etc. will infer from Probe_IDs if not given
genome

hg38, mm10, ... will infer if not given. For additional mapping, download the GRanges object from http://zwdzwd.github.io/InfiniumAnnotation and provide the following argument ..., genome = sesameAnno_buildManifestGRanges("downloaded_file"),... to this function.
silent

suppress messages

Details

For annotation by probe ID using KYCG databases (rather than by genomic coordinates), see knowYourCG::annoProbes()

Value

a GRanges with annotated column If a probe has no overlap with regs, it will be included in the results with NA. But if a probe is not included in the manifest (due to mappability), it won't be included in the results.

Examples

library(GenomicRanges)
sesameDataCache(c(
    "genomeInfo.mm10", "MM285.address",
    "genomeInfo.hg38", "Mammal40.address"))

## Example 1: Basic usage - annotate with gene names (default)
## When regs=NULL, function defaults to gene annotation
probes <- c("cg14620903", "cg22464003")
anno <- sesameData_annoProbes(probes)
## Returns GRanges with gene_name column

## Example 2: Annotate mouse probes with promoter regions
regs <- sesameData_getTxnGRanges("mm10")
Probe_IDs <- names(sesameData_getManifestGRanges("MM285"))[1:100]
anno <- sesameData_annoProbes(Probe_IDs, promoters(regs), column="gene_name")
## Probes overlapping promoters are annotated with gene names

## Example 3: Get features that overlap with probes
## return_ov_features=TRUE returns the overlapping genomic features
genes <- sesameData_getTxnGRanges("hg38", merge2gene = TRUE)
ov_genes <- sesameData_annoProbes(
    c("cg14620903","cg22464003"), genes, return_ov_features=TRUE)
## Returns GRanges of genes overlapping the probes

## Example 4: Get probes that overlap with features
## return_ov_probes=TRUE returns only overlapping probes
ov_probes <- sesameData_annoProbes(
    c("cg14620903","cg22464003"), genes, return_ov_probes=TRUE)
## Returns GRanges of probes that overlap genes

## Example 5: Control annotation collapsing behavior
## collapse=TRUE (default): multiple annotations concatenated with separator
anno_collapsed <- sesameData_annoProbes(
    c("cg14620903","cg22464003"), genes, column="gene_name",
    collapse=TRUE, sep=";")
## Multiple overlapping genes listed as "GENE1;GENE2;GENE3"

## collapse=FALSE: each probe-feature overlap gets separate entry
anno_expanded <- sesameData_annoProbes(
    c("cg14620903","cg22464003"), genes, column="gene_name",
    collapse=FALSE)
## Probes with multiple overlaps appear multiple times

## Example 6: Choose only first annotation when multiple exist
anno_one <- sesameData_annoProbes(
    c("cg14620903","cg22464003"), genes, column="gene_name",
    chooseOne=TRUE)
## Each probe gets only the first overlapping gene

## Example 7: Annotate with custom genomic regions
custom_regs <- GRanges(
    seqnames = c("chr5", "chr5"),
    ranges = IRanges(start = c(10000, 135350870),
                     end = c(135350866, 145369531)),
    feature_type = c("enhancer", "silencer"))
anno_custom <- sesameData_annoProbes(
    c("cg14620903","cg22464003"), custom_regs,
    column="feature_type", genome="hg38")

## Note: For annotation by probe ID using KYCG databases
## (rather than genomic coordinates), see knowYourCG::annoProbes()

Find genome assembly version(s) supported for a platform

Description

Find genome assembly version(s) supported for a platform

Usage

sesameData_check_genome(genome, platform)

Arguments

genome

mm10, hg38, ..., or NULL
platform

HM27, HM450, EPIC, EPICv2, MSA, ...

Value

genome as string

Examples

sesameData_check_genome(NULL, "Mammal40")

Check platform code

Description

Note: custome platforms lead to error here.

Usage

sesameData_check_platform(platform = NULL, probes = NULL, silent = TRUE)

Arguments

platform

input platform
probes

probes by which the platform may be guessed
silent

suppress message

Value

platform code

Examples

sesameData_check_platform("HM450")

Get genome info files

Description

Get genome info files

Usage

sesameData_getGenomeInfo(genome)

Arguments

genome

hg38, mm10, or GRanges with a metadata(genome)[["genome"]]

Value

a list of genome info files

Examples

sesameDataCache("genomeInfo.hg38")
res <- sesameData_getGenomeInfo("hg38")

get Infinium manifest GRanges

Description

Note that some unaligned probes are not included. For full manifest, please visit http://zwdzwd.github.io/InfiniumAnnotation

Usage

sesameData_getManifestGRanges(platform, genome = NULL)

Arguments

platform

Mammal40, MM285, EPIC, and HM450
genome

hg38, mm10, ... will infer if not given. For additional mapping, download the GRanges object from http://zwdzwd.github.io/InfiniumAnnotation and provide the following argument ..., genome = sesameAnno_buildManifestGRanges("downloaded_file"),... to this function.

Value

GRanges

Examples

sesameDataCache("Mammal40.address")
res <- sesameData_getManifestGRanges("Mammal40")

Get Probes by Genes or Gene Promoters

Description

Get probes mapped to a gene. All transcripts for the gene are considered. The function takes a gene name as appears in UCSC RefGene database. The platform and reference genome build can be changed with 'platform' and 'genome' options. The function returns a vector of probes that falls into the given gene.

Usage

sesameData_getProbesByGene(
  gene_name = NULL,
  platform = NULL,
  promoter = FALSE,
  upstream = 1500,
  downstream = 1500,
  genome = NULL
)

Arguments

gene_name

gene name, if NULL return all genes
platform

EPIC or HM450
promoter

if TRUE, use TSS instead of the whole gene
upstream

number of bases to expand upstream of target gene
downstream

number of bases to expand downstream of target gene
genome

hg38 or hg19

Value

GRanges containing probes that fall into the given gene

Examples

## download needed data
sesameDataCache(c("Mammal40.address", "genomeInfo.hg38"))

## get all probes overlapping with DNMT3A
probes <- sesameData_getProbesByGene(
    'DNMT3A', "Mammal40", upstream=500, downstream=500)

## get the promoter-associated probes
probes <- sesameData_getProbesByGene('DNMT3A', "Mammal40", promoter = TRUE)

Get probes by genomic region

Description

The function takes a genomic coordinate and output the a vector of probes on the specified platform that falls in the given genomic region.

Usage

sesameData_getProbesByRegion(
  regs,
  chrm = NULL,
  beg = 1,
  end = -1,
  platform = NULL,
  chrm_to_exclude = NULL,
  genome = NULL
)

Arguments

regs

GRanges
chrm

chromosome, when given regs are ignored
beg

begin, 1 if omitted
end

end, chromosome end if omitted
platform

EPICv2, EPIC, HM450, ...
chrm_to_exclude

chromosome to exclude.
genome

hg38, mm10, ... will infer if not given. For additional mapping, download the GRanges object from http://zwdzwd.github.io/InfiniumAnnotation and provide the following argument ..., genome = sesameAnno_buildManifestGRanges("downloaded_file"),... to this function.

Value

GRanges of selected probes

Examples

## download needed data
sesameDataCache(c("Mammal40.address", "genomeInfo.hg38"))

## get probes in a region
library(GenomicRanges)
probes = sesameData_getProbesByRegion(
    GRanges('chr5', IRanges(135313937, 135419936)), platform = 'Mammal40')

## get all probes on chromosome 5
probes = sesameData_getProbesByRegion(chrm = "chr5", platform = "Mammal40")

## get all probes on chromosome X
probes = sesameData_getProbesByRegion(chrm = 'chrX', platform = "Mammal40")

## get all probes on both chromosome X and Y
probes = sesameData_getProbesByRegion(
    chrm = c('chrX', 'chrY'), platform = "Mammal40")

## get all autosomal probes
probes = sesameData_getProbesByRegion(
    chrm_to_exclude = c("chrX", "chrY"), platform = "Mammal40")

convert GRangesList to transcript GRanges

Description

convert GRangesList to transcript GRanges

Usage

sesameData_getTxnGRanges(genome = NULL, grl = NULL, merge2gene = FALSE)

Arguments

genome

hg38, mm10, ...
grl

GRangesList object
merge2gene

merge transcript to genes

Value

a GRanges object

Examples

## all mm10 transcripts
txns <- sesameData_getTxnGRanges("mm10")

## verified protein-coding transcripts
txns[(txns$transcript_type == "protein_coding" & txns$level <= 2)]

## merged to genes
sesameData_getTxnGRanges("mm10", merge2gene = TRUE)

convert transcript GRanges to gene GRanges

Description

convert transcript GRanges to gene GRanges

Usage

sesameData_txnToGeneGRanges(txns)

Arguments

txns

GRanges object

Value

a GRanges object

Examples

txns <- sesameData_getTxnGRanges("mm10")
genes <- sesameData_txnToGeneGRanges(txns)

Cache SeSAMe data

Description

Cache SeSAMe data

Usage

sesameDataCache(data_titles = NULL)

Arguments

data_titles

data to cache, if not given will cache all

Value

TRUE

Examples

sesameDataCache("genomeInfo.hg38")

Cache all SeSAMe data

Description

Cache all SeSAMe data

Usage

sesameDataCacheAll(data_titles = NULL)

Arguments

data_titles

data to cache, if not given will cache all

Value

TRUE

Examples

sesameDataCache("genomeInfo.hg38")

Get SeSAMe data

Description

Get SeSAMe data

Usage

sesameDataGet(title, verbose = FALSE)

Arguments

title

title of the data
verbose

whether to output ExperimentHub message

Value

data object

Examples

sesameDataCache("EPIC.1.SigDF")
EPIC.1.SigDF <- sesameDataGet('EPIC.1.SigDF')

Check whether the title exists in cacheEnv

Description

Check whether the title exists in cacheEnv

Usage

sesameDataGet_checkEnv(title)

Arguments

title

the title to check

Value

the data associated with the title or NULL if title doesn't exist

Empty cache environment to free memory

Description

When this function is called sesameDataGet will retrieve all data from disk again instead of using the in-memory cache, i.e., sesameData:::cacheEnv.

Usage

sesameDataGet_resetEnv()

Details

Note this is different from sesameDataClearHub which empties the ExperimentHub on disk.

Value

gc() output

Examples

sesameDataGet_resetEnv()

Whether sesameData has

Description

Whether sesameData has

Usage

sesameDataHas(data_titles)

Arguments

data_titles

data titles to check

Value

a boolean vector the same length as data_titles

Examples

sesameDataHas(c("EPIC.address","EPIC.address.Nonexist"))

List all SeSAMe data

Description

List all SeSAMe data

Usage

sesameDataList(filter = NULL, full = FALSE)

Arguments

filter

keyword to filter title, optional
full

whether to display all columns

Value

all titles from SeSAMe Data

Examples

sesameDataList("KYCG")