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Rank the Abundance from a File or Data Frame

Source: R/BC_rank.R
BC_rank.Rd

Sorts the df_abundance dataframe by the given column argument.

Usage

BC_rank(df_abundance, column, rank_threshold = 0, is_phyloseq = FALSE, ...)

Arguments

df_abundance

The data frame to use. A string that contains a path can be used to load files.

column

Can be either a string containing the name of the column or an int that is its index

rank_threshold

Optional. Integer. Discards rows if their column value is equal to or lower than it. Defaults to 0.

is_phyloseq

Logical, optional. Use if the object to be analysed has the phyloseq class.

...

passes arguments to read.table.

Value

The input data frame with a column appended to the left that stores the generated ranking. The column used for ranking is renamed "abundance".

Examples

rankedWeblinks <- BC_rank(df_abundance=DGBD::Weblinks, column=2, rank_threshold=4)
head(rankedWeblinks)
#>   BC_rank degree abundance
#> 1       3      0  35159835
#> 2       1      1 106649769
#> 3       2      2  40711748
#> 4       4      3  22648832
#> 5       5      4  12617832
#> 6       6      5   8188854

rankedTara <- BC_rank(Tara_Data,3,is_phyloseq=TRUE)
head(rankedTara)
#>         BC_rank MGYA00133816 MGYA00133817 abundance
#> 941278      195            7           11         8
#> 769551      138            1           15        14
#> 4165717     620            1            0         1
#> 1111505     179            1           17         9
#> 1111241      80            7            5        28
#> 576629       43            1           33        52