drop_uninformative_genes {EWCE} | R Documentation |
drop_uninformative_genes
drops genes from an SCT expression matrix
if they do not significantly vary between any celltypes.
Makes this decision based on use of an ANOVA (implemented with Limma). If
the F-statistic for variation amongst type2 annotations
is less than a strict p-threshold, then the gene is dropped.
drop_uninformative_genes(exp, level2annot)
exp |
Expression matrix with gene names as rownames. |
level2annot |
Array of cell types, with each sequentially corresponding a column in the expression matrix |
exp Expression matrix with gene names as rownames.
library(ewceData) cortex_mrna <- cortex_mrna() cortex_mrna$exp <- cortex_mrna$exp[1:300, ] exp2 <- drop_uninformative_genes(exp = cortex_mrna$exp, level2annot = cortex_mrna$annot$level2class)