could not find function "SigSetsToRGChannelSet"

[yyuu33nn]

help, im trying to convert SigSet to RGset , however i keep getting such message:

> SigSetsToRGChannelSet(betas_list, BPPARAM = SerialParam(), annotation = NA)
Error in SigSetsToRGChannelSet(betas_list, BPPARAM = SerialParam(), annotation = NA) : 
  could not find function "SigSetsToRGChannelSet"
> View(sdfs)
> SigSetsToRGChannelSet(betas_list)
Error in SigSetsToRGChannelSet(betas_list) : 
  could not find function "SigSetsToRGChannelSet"

and when i check > exists("SigSetsToRGChannelSet", where = getNamespace("sesame")) i got a : [1] FALSE

what i have done: remove all RData and reinstall the latest bioconductor and zwdzwd/sesame. able to read and preprocess the sigset.

Im trying to access the EPIC V2 Chip data, so i can input it into my epigenetic clock pipelines and calculate the age. following is my full code:

if (!requireNamespace("BiocManager", quietly = TRUE))
  install.packages("BiocManager")
BiocManager::install("zwdzwd/sesame", force=TRUE)

library(sesame)
exists("SigSetsToRGChannelSet", where = getNamespace("sesame"))

sesameDataCache()
tools::R_user_dir("ExperimentHub", which="cache")

# Define the path to the IDAT files
idat_path <- "/Mypath_to_IDATs"

# Search for IDAT prefixes in the specified path
idat_prefixes <- searchIDATprefixes(idat_path)

# Read each IDAT pair using lapply and the readIDATpair function
sdfs <- lapply(idat_prefixes, readIDATpair)

# To check the output
# Apply the head function to the first few elements of the list to view their contents
lapply(sdfs[1:8], head)

# Preprocessing function for IDAT files
process_idat_files <- function(data) {
  # No need to read IDAT files here, 'data' is already loaded by 'readIDATpair'
  data <- qualityMask(data)
  data <- inferInfiniumIChannel(data)
  data <- dyeBiasNL(data)
  data <- pOOBAH(data)
  betas <- getBetas(noob(data))

  return(betas)
}

# Apply the corrected preprocessing function to each loaded IDAT pair in sdfs
betas_list <- lapply(sdfs, process_idat_files)

# To see the beta values for the first few probes of the first sample
head(betas_list[[1]])

SigSetsToRGChannelSet(betas_list, BPPARAM = SerialParam(), annotation = NA)

[zwdzwd]

since SigSet is no longer supported. have you tried using SigDF and the updated sesamize function? https://github.com/zwdzwd/sesamize/blob/main/sesamize.R and https://zhou-lab.github.io/sesame/dev/supplemental.html#Interaction_with_Other_Tools ?

[zwdzwd]

Sorry, I am a bit confused, the input to SigDFsToRGChannelSet should be a list of SigDF. No need to process it to beta values. Whether to apply any preprocessing depends on need.

[tamefelis]

Dear Wanding,

however when we wish to proceed with the list of SigDF, the Function had failed.

or code, really appreciate if we can have your input here. :

+   
+   if (is(sdfs, 'SigDF')) {
+     sdfs <- list(sample=sdfs)
+   }
+   
+   pt <- sdfPlatform(sdfs[[1]])
+   annotation <- guessMinfiAnnotation(pt, annotation)
+   
+   ss_all <- bplapply(sdfs, SigDFToRGChannel, BPPARAM=BPPARAM)
+   rgset <- minfi::RGChannelSet(
+     Green=do.call(cbind, lapply(ss_all, function(ss) ss$grn)), 
+     Red=do.call(cbind, lapply(ss_all, function(ss) ss$red)), 
+     annotation=c(
+       array=unname(platformSmToMinfi(pt)),
+       annotation=annotation))
+ }
> SigDFsToRGChannelSet(sdfs)
Error: BiocParallel errors
  1 remote errors, element index: 1
  7 unevaluated and other errors
  first remote error:
Error in InfI(sdf): could not find function "InfI"
Called from: .bpinit(manager = manager, X = X, FUN = FUN, ARGS = ARGS, BPPARAM = BPPARAM, 
    BPOPTIONS = BPOPTIONS, BPREDO = BPREDO)```

[altuda]

Hi, I am also struggling with Sesamize/RGChannelSetToSigDFs. Your contributions to Sesame are invaluable, and I would be grateful for your assistance with this issue. Thank you for all the work you've done.

grSet <- RGChannelSetToSigDFs(FlowSorted.Blood.450k[,1:4]) Error: BiocParallel errors 1 remote errors, element index: 1 3 unevaluated and other errors first remote error: Error in chipAddressToSignal(dm, manifest): could not find function "chipAddressToSignal"

approach according to vignette

grSet <- sesamize(FlowSorted.Blood.450k[,1:4]) Sesamizing 1... Sesamizing 1... Error in (function (classes, fdef, mtable) : unable to find an inherited method for function ‘mapToGenome’ for signature ‘"matrix"’

str(FlowSorted.Blood.450k) Formal class 'RGChannelSet' [package "minfi"] with 6 slots...