Remove samples from a Dataset object.

Remove samples from a Dataset object.

remove_samples(Dat, samples, droplevels = TRUE)

Arguments

Dat	A Dataset object
samples	String vector indicating which samples to remove. Sample IDs must be equal to the column headers of the abundance table on Dat.
droplevels	Logical indicating whether levels that desappear from the mapping file should be removed.

Value

A Dataset object

See also

remove_taxons

Examples

data(Rhizo)
data(Rhizo.map)
Dat <- create_dataset(Rhizo,Rhizo.map)
Dat <- remove_samples(Dat = Dat,
                      samples = colnames(Dat$Tab)[1:50])
Dat <- remove_taxons(Dat = Dat,
                     taxons = row.names(Dat$Tab)[1:115])

sum(colSums(Dat$Tab) == 0)
#> [1] 3
sum(rowSums(Dat$Tab) == 0)
#> [1] 1

Dat$Tab
#>           D429 D447 D448 D449 D450 D451 D452 D453 D454 D455 D456 D678 D679 D680
#> OTU_19916    0    0    0    0    1    0    1    0    0    0    0    1    0    0
#> OTU_6457     0    0    0    1    0    1    0    0    0    0    0    0    0    0
#> OTU_6024     0    0    0    0    0    1    0    0    0    0    0   14    3   12
#> OTU_14844    0    0    0    0    0    0    0    0    0    0    0   10    5   13
#> OTU_18380    0    1    0    0    0    0    0    0    0    0    0    0    0    0
#> OTU_14780    0    0    0    0    0    0    0    0    0    0    0    4    1    3
#> OTU_20070    0    0    0    0    0    0    0    0    1    0    0    2   10    4
#> OTU_19960    0    0    1    0    0    0    0    0    0    0    0    1    0    0
#> OTU_12223    0    0    0    0    0    1    0    0    0    0    2    3    1    7
#> OTU_18927    0    0    0    0    0    0    1    0    0    0    0    1    8    1
#> OTU_19093    0    0    0    0    0    0    0    0    0    0    0   35    3    4
#> OTU_11949    0    0    0    0    0    0    0    0    0    0    0    2   14    6
#> OTU_7118     0    0    0    0    0    0    0    0    0    0    0    0    0    0
#> OTU_16233    0    0    0    0    0    0    0    0    0    0    0    0    0    0
#>           D681 D682 D1045 D1046 D1047
#> OTU_19916    1    0     0     0     0
#> OTU_6457     0    0     0     0     0
#> OTU_6024    38   25    28     8     3
#> OTU_14844   43   10    11    12     2
#> OTU_18380    0    0     1     0     0
#> OTU_14780   19    8    11     0    11
#> OTU_20070    1   10     2    21     6
#> OTU_19960    0    0     0     0     0
#> OTU_12223    3    3     3     0     0
#> OTU_18927    5    6     1     1     3
#> OTU_19093   10    2     6     4     3
#> OTU_11949    2    4    10    19     1
#> OTU_7118     1    0     0     0     0
#> OTU_16233    0    0     0     0     0
Dat.clean <- clean(Dat)
#> 3 samples removed
#> 1 taxons removed
Dat.clean$Tab
#>           D447 D448 D449 D450 D451 D452 D454 D456 D678 D679 D680 D681 D682
#> OTU_19916    0    0    0    1    0    1    0    0    1    0    0    1    0
#> OTU_6457     0    0    1    0    1    0    0    0    0    0    0    0    0
#> OTU_6024     0    0    0    0    1    0    0    0   14    3   12   38   25
#> OTU_14844    0    0    0    0    0    0    0    0   10    5   13   43   10
#> OTU_18380    1    0    0    0    0    0    0    0    0    0    0    0    0
#> OTU_14780    0    0    0    0    0    0    0    0    4    1    3   19    8
#> OTU_20070    0    0    0    0    0    0    1    0    2   10    4    1   10
#> OTU_19960    0    1    0    0    0    0    0    0    1    0    0    0    0
#> OTU_12223    0    0    0    0    1    0    0    2    3    1    7    3    3
#> OTU_18927    0    0    0    0    0    1    0    0    1    8    1    5    6
#> OTU_19093    0    0    0    0    0    0    0    0   35    3    4   10    2
#> OTU_11949    0    0    0    0    0    0    0    0    2   14    6    2    4
#> OTU_7118     0    0    0    0    0    0    0    0    0    0    0    1    0
#>           D1045 D1046 D1047
#> OTU_19916     0     0     0
#> OTU_6457      0     0     0
#> OTU_6024     28     8     3
#> OTU_14844    11    12     2
#> OTU_18380     1     0     0
#> OTU_14780    11     0    11
#> OTU_20070     2    21     6
#> OTU_19960     0     0     0
#> OTU_12223     3     0     0
#> OTU_18927     1     1     3
#> OTU_19093     6     4     3
#> OTU_11949    10    19     1
#> OTU_7118      0     0     0