Cloud-based LOcally linear Unbiased Dysbiosis (CLOUD) test

Arguments

x: A phyloseq object
reference_samples: Vector of samples to use as reference.
dist_mat: A distance matrix. Can be output of phyloseq::distance or vegan::vegdist.
k_num: Neighbors to use. Default is 5 percent. User can define percent of samples. See Montassier E et al. 2018 for more details.
ndim: Dimension of the space in which the data are to be represented. Default is -1. See Montassier E et al. 2018

Value

A data frame with CLOUD stats and sample information

Details

Calculates CLOUD score.

Cloud-based LOcally linear Unbiased Dysbiosis (CLOUD) test is a non-parametric test and returns a measure of dysbiosis. The function was adapted from the original article by Montassier E et al. 2018. Here, a user defines a set of reference samples from which distance of every other sample is calculated. When calculating the CLOUD stats the k is an important parameter specified by argument k_num. By default we use a conservative 80 percent of the samples in each group.

References

Montassier E et al. (2018). CLOUD: a non-parametric detection test for microbiome outliers. Microbiome, 6(1), pp.1-10.

Author

Sudarshan A. Shetty

Examples

data("WirbelJ_2018")
library(phyloseq)
ps <- WirbelJ_2018
# Define controls as reference samples
ref.samples <- sample_names(subset_samples(WirbelJ_2018,
                                           disease == "healthy"))
dist.data <- phyloseq::distance(ps, "bray")
cloud.results <- cloudStatistic(x= ps,
                                dist_mat = dist.data,
                                reference_samples = ref.samples,
                                ndim=-1,
                                k_num=5)
head(cloud.results)
#>                         stats pvals  log2Stats   study_name          subject_id
#> CCMD10032470ST-11-0 0.6673767     1 -0.5834267 WirbelJ_2018 CCMD10032470ST-11-0
#> CCMD10191450ST-11-0 0.6603512     1 -0.5986947 WirbelJ_2018 CCMD10191450ST-11-0
#> CCMD11006829ST-21-0 0.8141492     1 -0.2966349 WirbelJ_2018 CCMD11006829ST-21-0
#> CCMD12232071ST-21-0 0.7767293     1 -0.3645161 WirbelJ_2018 CCMD12232071ST-21-0
#> CCMD13071240ST-21-0 0.7656822     1 -0.3851824 WirbelJ_2018 CCMD13071240ST-21-0
#> CCMD13934959ST-21-0 0.6943361     1 -0.5262940 WirbelJ_2018 CCMD13934959ST-21-0
#>                     body_site study_condition disease age age_category gender
#> CCMD10032470ST-11-0     stool         control healthy  45        adult   male
#> CCMD10191450ST-11-0     stool         control healthy  62        adult female
#> CCMD11006829ST-21-0     stool             CRC     CRC  42        adult female
#> CCMD12232071ST-21-0     stool             CRC     CRC  75       senior   male
#> CCMD13071240ST-21-0     stool             CRC     CRC  66       senior female
#> CCMD13934959ST-21-0     stool             CRC     CRC  56        adult   male
#>                     country non_westernized sequencing_platform
#> CCMD10032470ST-11-0     DEU              no       IlluminaHiSeq
#> CCMD10191450ST-11-0     DEU              no       IlluminaHiSeq
#> CCMD11006829ST-21-0     DEU              no       IlluminaHiSeq
#> CCMD12232071ST-21-0     DEU              no       IlluminaHiSeq
#> CCMD13071240ST-21-0     DEU              no       IlluminaHiSeq
#> CCMD13934959ST-21-0     DEU              no       IlluminaHiSeq
#>                     DNA_extraction_kit     PMID number_reads number_bases
#> CCMD10032470ST-11-0              Gnome 30936547     37708359   4639213592
#> CCMD10191450ST-11-0              Gnome 30936547     34952407   4351849639
#> CCMD11006829ST-21-0              Gnome 30936547     83456496   7310970279
#> CCMD12232071ST-21-0              Gnome 30936547     65269931   5370021950
#> CCMD13071240ST-21-0              Gnome 30936547     63427722   5486983593
#> CCMD13934959ST-21-0              Gnome 30936547     36979669   3186342244
#>                     minimum_read_length median_read_length NCBI_accession
#> CCMD10032470ST-11-0                  45                139     ERR2726404
#> CCMD10191450ST-11-0                  45                140     ERR2726405
#> CCMD11006829ST-21-0                  45                 94           <NA>
#> CCMD12232071ST-21-0                   2                 88           <NA>
#> CCMD13071240ST-21-0                  45                 93           <NA>
#> CCMD13934959ST-21-0                  45                 93           <NA>
#>                                       curator  BMI    tnm ajcc nspecies   group
#> CCMD10032470ST-11-0 Jacob_Wirbel;Paolo_Manghi 30.7   <NA> <NA>       72 control
#> CCMD10191450ST-11-0 Jacob_Wirbel;Paolo_Manghi 28.5   <NA> <NA>       87 control
#> CCMD11006829ST-21-0              Paolo_Manghi 35.0 t3n0m0   ii      144    case
#> CCMD12232071ST-21-0              Paolo_Manghi 28.0 t3n2m0  iii      110    case
#> CCMD13071240ST-21-0              Paolo_Manghi 23.0 t3n0m0   ii      126    case
#> CCMD13934959ST-21-0              Paolo_Manghi 27.0 t3n0m0   ii      100    case