Filter to retain only taxa with at least abund_thresh counts in at least sample_thresh samples
Usage
filter_low_count(
countdata,
metadata,
abund_thresh = 5,
sample_thresh = 3,
sample_colname,
group_colname
)
Arguments
- countdata
otu table
- metadata
dataframe with 2 rows sample names and group names
- abund_thresh
minimum number of taxa abundance threshold
- sample_thresh
minimum number of sample threshold
- sample_colname
column names of the samples
- group_colname
column names of the groups or conditions
Value
filtered otu count data