Prints a short summary of a geneda object: the number of features,
samples, and HVGs, whether PCA results and counts are present, and the
names of stored DEG tables.
Usage
# S4 method for class 'geneda'
show(object)Examples
data(Snail1KO)
counts <- as.matrix(Snail1KO$rawCounts)
counts <- counts[rowSums(counts >= 10) >= 3, ]
meta <- Snail1KO$metadata
rownames(meta) <- meta$Sample
norm <- log2(t(t(counts) / colSums(counts)) * 1e6 + 1)
obj <- GenEDA(normalized = norm, metadata = meta, counts = counts)
obj <- RunPCA(obj, nfeatures = 1000)
#> HVG slot is empty. Running FindVariableFeatures with top 1000 genes
#> Calculating principal components from top 1000 HVGs
#> Percent variations:
#> PC1: 88.56 %
#> PC2: 5.9 %
#> PC3: 2.91 %
#> PC4: 1.55 %
#> PC5: 1.08 %
#> PC6: 0 %
show(obj)
#> geneda object
#> features: 11247
#> samples: 6
#> HVGs: 1000
#> DimReduction: 3
#> counts: present
#> DEGs: none