Add QC statistics to the Spatial Experiment object
addPerROIQC(
spe_object,
sample_fraction = 0.9,
rm_genes = TRUE,
min_count = 5,
design = NULL
)A SpatialExperiment object
Double. Genes with low count in more than this threshold of the samples will be removed. Default is 0.9
Logical. Decide whether genes with low count in more than sample_fraction of the samples are removed from the dataset. Default is TRUE.
Integer. Minimum read count to calculate count threshold. Default is 5.
Generate using model.matrix, if this is specify, edgeR::filterByExpr will be used to filter genes.
A SpatialExperiment object
data("dkd_spe_subset")
spe_filtered <- addPerROIQC(dkd_spe_subset)
#> Loading required package: SpatialExperiment
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spe_filtered
#> class: SpatialExperiment
#> dim: 2978 70
#> metadata(4): NegProbes lcpm_threshold genes_rm_rawCount genes_rm_logCPM
#> assays(2): counts logcounts
#> rownames(2978): TMIGD2 DOCK1 ... CLDN2 NR2C2AP
#> rowData names(4): RTS_ID ProbeID Negative genes_lowCount_overNsamples
#> colnames(70): disease3_scan | 003 | neg disease3_scan | 050 | Geometric
#> Segment ... disease3_scan | 009 | Geometric Segment normal3_scan |
#> 002 | PanCK
#> colData names(28): SlideName ScanName ... countOfLowEprGene
#> percentOfLowEprGene
#> reducedDimNames(0):
#> mainExpName: NULL
#> altExpNames(0):
#> spatialCoords names(2) : ROICoordinateX ROICoordinateY
#> imgData names(1): sample_id