Apply num.sv algorithm to determine the number of pcs to be included
k_qsvs(rse_tx, mod, assayname)A RangedSummarizedExperiment-class object containing the transcript data desired to be studied.
Model Matrix with necessary variables the you would model for in differential expression
character string specifying the name of the assay desired in rse_tx
integer representing number of pcs to be included
## First we need to define a statistical model. We'll use the example
## rse_tx data. Note that the model you'll use in your own data
## might look different from this model.
mod <- model.matrix(~ mitoRate + Region + rRNA_rate + totalAssignedGene + RIN,
data = colData(rse_tx)
)
## To ensure that the results are reproducible, you will need to set a
## random seed with the set.seed() function. Internally, we are using
## sva::num.sv() which needs a random seed to ensure reproducibility of the
## results.
set.seed(20230621)
k_qsvs(rse_tx, mod, "tpm")
#> [1] 10