Get regressed data
Usage
get_regressed_data(
sum_exp,
assay_to_use,
which_pca = "big",
stable_genes = NULL,
remove_components = c("PC1", "PC2", "PC5")
)Arguments
- sum_exp
Summarized experiment object. It should contain a "rank" slot that will be used to calculate the average rank of the stable genes.
- assay_to_use
A string. Which assay to use when calculating the average expression of the stable genes.
- which_pca
A string stating which PCA object to use to get the coordinates. Two options available: "small" or "big". The "small" option uses the fit with only 1044 genes. The "big" option uses the one with all the 8000+ genes, used for the regression of the data.
- stable_genes
A vector. A list with 44 genes that will be used to the qPCR-like normalization if NULL (default).
- remove_components
A vector with the principal components to be removed. Default is PC1, PC2 and PC5