Abundance table for 199 samples.

A dataset containing the abundances of 1585 lineages among 199 patients.

Usage

abundances

Format

A data.frame with 1585 rows and 200 variables:

lineages

lineage (string)

XXX

abundance of each lineage in the sample XXX (double)

Source

Zeller et al., 2014 (doi:10.15252/msb.20145645 ), Pasolli et al., 2017 (doi:10.1038/nmeth.4468 ).

Examples

dim(abundances)
#> [1] 1585  200
abundances[1:5, 1:7]
#>                        lineages CCIS00146684ST-4-0 CCIS00281083ST-3-0
#> 1                   k__Bacteria           99.99303           99.77420
#> 2                    k__Viruses            0.00697            0.12845
#> 3     k__Bacteria|p__Firmicutes           66.22353           24.55047
#> 4  k__Bacteria|p__Bacteroidetes           19.08010           74.36025
#> 5 k__Bacteria|p__Actinobacteria           12.06619            0.04278
#>   CCIS02124300ST-4-0 CCIS02379307ST-4-0 CCIS02856720ST-4-0 CCIS03473770ST-4-0
#> 1           96.29863           99.93664           97.60238           94.05719
#> 2            3.70137            0.00471            2.39282            1.10214
#> 3           74.16762           45.09844           64.59344           63.38280
#> 4           11.86757           52.96156           22.64060           21.67989
#> 5            7.21542            0.07885            1.72788            4.65559