xiangpin
commented
1 year ago You can try a larger min.abun value and include.lowest=T (meaning >= min.abun) or include.lowest=F (meaning >min.abun), and you can extract the specified assay to make statistics.
> mouse.time.mpse %>% mp_extract_assays(.abundance=Abundance) %>% `>`(1) %>% table()
.
FALSE TRUE
2521 1621
> mouse.time.mpse %>% mp_extract_assays(.abundance=Abundance) %>% `>=`(1) %>% table()
.
FALSE TRUE
2521 1621
> mouse.time.mpse %>% mp_extract_assays(.abundance=Abundance) %>% `>`(2) %>% table()
.
FALSE TRUE
2535 1607
> mouse.time.mpse %>% mp_extract_assays(.abundance=Abundance) %>% `>=`(2) %>% table()
.
FALSE TRUE
2521 1621
> mouse.time.mpse %>% mp_extract_assays(.abundance=Abundance) %>% `>`(3) %>% table()
.
FALSE TRUE
2570 1572
> mouse.time.mpse %>% mp_extract_assays(.abundance=Abundance) %>% `>=`(3) %>% table()
.
FALSE TRUE
2535 1607
> mouse.time.mpse %>% mp_extract_assays(.abundance=Abundance) %>% `>`(4) %>% table()
.
FALSE TRUE
2609 1533
> mouse.time.mpse %>% mp_extract_assays(.abundance=Abundance) %>% `>=`(4) %>% table()
.
FALSE TRUE
2570 1572
When I use the
mp_filter_taxafunction, I found thatinclude.lowestseems not work, which always return theinclude.lowest=Falsereuslt. However, when try it using example datasetmouse.time.mpse, it works fine. I could not figure out why but I think this is very important, because many users may not notice this. My dataset is unpublic, so if you need it to test, welcome to contact me.