mLiftOver: Lift over beta values or SigDFs to another Infinium platform...

In zwdzwd/sesame: SEnsible Step-wise Analysis of DNA MEthylation BeadChips

Lift over beta values or SigDFs to another Infinium platform This function wraps ID conversion and provide optional imputation functionality.

Description

Lift over beta values or SigDFs to another Infinium platform This function wraps ID conversion and provide optional imputation functionality.

Usage

mLiftOver(
  x,
  target_platform,
  source_platform = NULL,
  BPPARAM = SerialParam(),
  mapping = NULL,
  impute = FALSE,
  sd_max = 999,
  celltype = "Blood",
  ...
)

Arguments

x	either named beta value (vector or matrix), probe IDs or SigDF(s) if input is a matrix, probe IDs should be in the row names if input is a numeric vector, probe IDs should be in the vector names. If input is a character vector, the input will be considered probe IDs.
target_platform	the platform to take the data to
source_platform	optional information of the source data platform (when there might be ambiguity).
BPPARAM	use MulticoreParam(n) for parallel processing
mapping	a liftOver mapping file. Typically this file contains empirical evidence whether a probe mapping is reliable. If given, probe ID-based mapping will be skipped. This is to perform more stringent probe ID mapping.
impute	whether to impute or not, default is FALSE
sd_max	the maximum standard deviation for filtering low confidence imputation.
celltype	the cell type / tissue context of imputation, if not given, will use nearest neighbor to find out.
...	extra arguments, see ?convertProbeID

Value

imputed data, vector, matrix, SigDF(s)

Examples

## Not run: 
sesameDataCache()

## lift SigDF

sdf = sesameDataGet("EPICv2.8.SigDF")[["GM12878_206909630042_R08C01"]]
dim(mLiftOver(sdf, "EPICv2"))
dim(mLiftOver(sdf, "EPIC"))
dim(mLiftOver(sdf, "HM450"))

sdfs = sesameDataGet("EPICv2.8.SigDF")[1:2]
sdfs_hm450 = mLiftOver(sdfs, "HM450")
## parallel processing
sdfs_hm450 = mLiftOver(sdfs, "HM450", BPPARAM=BiocParallel::MulticoreParam(2))

sdf = sesameDataGet("EPIC.5.SigDF.normal")[[1]]
dim(mLiftOver(sdf, "EPICv2"))
dim(mLiftOver(sdf, "EPIC"))
dim(mLiftOver(sdf, "HM450"))

sdf = sesameDataGet("HM450.10.SigDF")[[1]]
dim(mLiftOver(sdf, "EPICv2"))
dim(mLiftOver(sdf, "EPIC"))
dim(mLiftOver(sdf, "HM450"))

## lift beta values

betas = openSesame(sesameDataGet("EPICv2.8.SigDF")[[1]])
betas_hm450 = mLiftOver(betas, "HM450", impute=TRUE)
length(betas_hm450)
sum(is.na(betas_hm450))
betas_hm450 <- mLiftOver(betas, "HM450", impute=FALSE)
length(betas_hm450)
sum(is.na(betas_hm450))
betas_epic1 <- mLiftOver(betas, "EPIC", impute=TRUE)
length(betas_epic1)
sum(is.na(betas_epic1))
betas_epic1 <- mLiftOver(betas, "EPIC", impute=FALSE)
length(betas_epic1)
sum(is.na(betas_epic1))

betas_matrix = openSesame(sesameDataGet("EPICv2.8.SigDF")[1:4])
dim(betas_matrix)
betas_matrix_hm450 = mLiftOver(betas_matrix, "HM450", impute=T)
dim(betas_matrix_hm450)
## parallel processing
betas_matrix_hm450 = mLiftOver(betas_matrix, "HM450", impute=T,
BPPARAM=BiocParallel::MulticoreParam(4))

## use empirical evidence in mLiftOver
mapping = sesameDataGet("liftOver.EPICv2ToEPIC")
betas_matrix = openSesame(sesameDataGet("EPICv2.8.SigDF")[1:4])
dim(mLiftOver(betas_matrix, "EPIC", mapping = mapping))
## compare to without using empirical evidence
dim(mLiftOver(betas_matrix, "EPIC"))

betas <- c("cg04707299"=0.2, "cg13380562"=0.9, "cg00000103"=0.1)
head(mLiftOver(betas, "HM450", impute=TRUE))

betas <- c("cg00004963_TC21"=0, "cg00004963_TC22"=0.5, "cg00004747_TC21"=1.0)
betas_hm450 <- mLiftOver(betas, "HM450", impute=TRUE)
head(na.omit(mLiftOver(betas, "HM450", impute=FALSE)))

## lift probe IDs

cg_epic2 = names(sesameData_getManifestGRanges("EPICv2"))
head(mLiftOver(cg_epic2, "HM450"))

cg_epic2 = grep("cg", names(sesameData_getManifestGRanges("EPICv2")), value=T)
head(mLiftOver(cg_epic2, "HM450"))

cg_hm450 = grep("cg", names(sesameData_getManifestGRanges("HM450")), value=T)
head(mLiftOver(cg_hm450, "EPICv2"))

rs_epic2 = grep("rs", names(sesameData_getManifestGRanges("EPICv2")), value=T)
head(mLiftOver(rs_epic2, "HM450", source_platform="EPICv2"))

probes_epic2 = names(sesameData_getManifestGRanges("EPICv2"))
head(mLiftOver(probes_epic2, "EPIC"))
head(mLiftOver(probes_epic2, "EPIC", target_uniq = TRUE))
head(mLiftOver(probes_epic2, "EPIC", include_new = FALSE))
head(mLiftOver(probes_epic2, "EPIC", include_old = FALSE))
head(mLiftOver(probes_epic2, "EPIC", return_mapping=TRUE))


## End(Not run)

zwdzwd/sesame documentation built on Dec. 21, 2024, 1:20 p.m.