Check format of input data and sample annotation, create a SummarizedExperiment object
Arguments
- data
A data frame with rows as features (e.g., genes, proteins) and columns as samples. The first column should contain feature identifiers (e.g., gene symbols) and named as 'Feature'. The data should have been log transformed (and normalised if needed). Missing values are allowed in some of the downstream analyses.
- sample_ann
A data frame containing sample annotations with required columns: 'Sample', 'Group', and 'Time'. 'Replicate' and 'Batch' are optional columns and will be set to 1 for all samples if not provided. 'Time', 'Replicate' and 'Batch' should be numeric.
Examples
data <- data.frame(Feature = c("Gene1", "Gene2"),
Sample1 = c(1, 2), Sample2 = c(3, 4))
sample_ann <- data.frame(
Sample = c("Sample1", "Sample2"),
Group = c("A", "A"),
Time = c(0, 1),
Replicate = c(1, 1),
Batch = c(1, 1)
)
se_obj <- create_input(data, sample_ann)
#> Converting 'Group' column to factor. Default order is alphabetical.
#> Converting 'Replicate' column to factor. Default order is numerical.
#> Converting 'Batch' column to factor. Default order is numerical.