pOverA / kOverA doesn't work…?

pOverA is a function that specifies the minimum count for a proportion of samples for each gene.

{r}
help(pOverA)

kOverA is a function that specifies the minimum count for a number of samples for each gene.

{r}
help(kOverA)

ex.

Suppose we want to select genes that have an expression measure above 200 in at least 5 samples. To do that we use the function kOverA.

There are three steps that must be performed.

Create function(s) implementing the filtering criteria.

Assemble it (them) into a (combined) filtering function.

Apply the filtering function to the expression matrix.

f1 <- kOverA(5, 200)
ffun <- filterfun(f1)
wh1 <- genefilter(exprs(sample.ExpressionSet), ffun)
sum(wh1)

## [1] 159

Here f1 is a function that implies our "expression measure above 200 in at least 5 samples" criterion, the function ffun is the filtering function (which in this case consists of only one criterion), and we apply it using r Biocpkg("genefilter"). There were 159 genes that satisfied the criterion and passed the filter.

genefilter

```{r}
# p is percent
pfilt <- (pOverA(0.3, 10))
pffun <- filterfun(pfilt)
pfilt_list <- genefilter(gcm, pffun)

pgkeep <- gcm[pfilt_list,]

nrow(gcm)
nrow(pgkeep)
```

```{r}
# k is number of samples
kfilt <- (kOverA(4, 10))
kffun <- filterfun(kfilt)
kfilt_list <- genefilter(gcm, kffun)

kgkeep <- gcm[kfilt_list,]

nrow(gcm)
nrow(kgkeep)
```

::: callout-warning
After filtering... we're left with very few (5!? really!?) genes that were expressed more than *only* 5 times in about a third of the samples ...this seems way off... even visually I can tell there are more than that when I scroll through the gene count matrix
:::