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Convert a TDRObj to SummarizedExperiment

Source: R/as-SummarizedExperiment.R
as.SummarizedExperiment.TDRObj.Rd

Converts a tinydenseR TDRObj into a SummarizedExperiment.

Usage

# S3 method for class 'TDRObj'
as.SummarizedExperiment(x, ...)

Arguments

x

A TDRObj (must have get.map completed).

...

Additional arguments (currently unused).

Value

A SummarizedExperiment.

Details

Rows represent tinydenseR landmarks (not genes/proteins). The assays stored are:

counts

Raw fuzzy graph density sums before size-factor normalization, from @density$raw.

normcounts

Size-factor-normalized fuzzy density (landmarks × samples), from @density$norm.

logcounts

log2(normcounts + 0.5), used by get.lm for linear modeling, from @density$log.norm.

rowData contains all stored clustering and celltyping solutions. colData contains sample-level metadata. The full TDRObj is preserved in metadata(se)$tdr.obj for downstream tinydenseR analysis via GetTDR.

See also

GetTDR, RunTDR

Examples

if (FALSE) { # \dontrun{
# Convert TDRObj to SummarizedExperiment
se <- as.SummarizedExperiment(tdr.obj)

# Access density data
SummarizedExperiment::assay(se, "logcounts")[1:5, 1:5]

# Round-trip: extract TDRObj for full tinydenseR analysis
tdr <- GetTDR(se)
} # }