Function to count how many genes are aligned with multiple factors.
Arguments
- factor_features
A
data.frameas returned by getAlignedFeatures.
Value
A data.frame for each factor pair with the numbers and proportions
of the genes in the input that overlap.
Examples
# Get a random matrix with rnorm, with 100 rows (features)
# and 20 columns (observations)
X <- ReducedExperiment:::.makeRandomData(100, 20, "feature", "obs")
# Estimate 5 factors based on the data matrix
fe <- estimateFactors(X, nc = 5)
# Get the genes highly aligned with each factor
aligned_features <- getAlignedFeatures(
fe,
format = "data.frame",
proportional_threshold = 0.3
)
# Identify overlap between common features for each factor
common_features <- getCommonFeatures(aligned_features)
head(common_features)
#> c_1 c_2 intersect total_feat_1 total_feat_2 smaller_total
#> 1 factor_1 factor_1 NA 8 8 8
#> 2 factor_1 factor_2 1 8 27 8
#> 3 factor_1 factor_3 0 8 10 8
#> 4 factor_1 factor_4 0 8 8 8
#> 5 factor_1 factor_5 2 8 30 8
#> 6 factor_2 factor_1 1 27 8 8
#> intersect_prop
#> 1 NA
#> 2 0.125
#> 3 0.000
#> 4 0.000
#> 5 0.250
#> 6 0.125