Read an .h5mu file and create a QFeatures object.

Read an .h5mu file and create a QFeatures object.

Usage

readLinkH5MU(path, feature_mapping_key = "feature_mapping", backed = FALSE)

Arguments

path

Path to the .h5mu file.

feature_mapping_key

Key of the feature graph in the global .varp.

backed

Passed to MuData::readH5MU().

Value

A QFeatures object. Assays and their links come from the file; if the .varp key is absent the sets are returned unlinked.

Limitations

Missing numeric values written as NA or NaN are read as NaN. The original distinction between NA and NaN is not preserved. See writeLinkH5MU() for other limitations of the write/read conversion.

Examples

data("feat3", package = "QFeatures")
preparedFeat3 <- prepareQFeatures(feat3)
#> Warning: Prefixed feature row names with assay names because they were not globally unique across the QFeatures object.
filePath <- tempfile(fileext = ".h5mu")
writeLinkH5MU(preparedFeat3, filePath)
newQFeatures <- readLinkH5MU(filePath)
#> Warning: sampleMap[['assay']] coerced with as.factor()
newQFeatures
#> An instance of class QFeatures (type: bulk) with 7 sets:
#> 
#>  [1] psms1: SummarizedExperiment with 7 rows and 2 columns 
#>  [2] psms2: SummarizedExperiment with 8 rows and 2 columns 
#>  [3] psmsall: SummarizedExperiment with 10 rows and 4 columns 
#>  [4] peptides: SummarizedExperiment with 3 rows and 4 columns 
#>  [5] proteins: SummarizedExperiment with 2 rows and 4 columns 
#>  [6] normpeptides: SummarizedExperiment with 3 rows and 4 columns 
#>  [7] normproteins: SummarizedExperiment with 2 rows and 4 columns 
unlink(filePath)