Combined Alpha Beta Diveristy Based Score
Details
Calculates a dysbiosis score that combined Shannon diversity and Jensen–Shannon divergence.
The combined alpha-beta diversity approach was used by
Santiago M E et al. 2019. This approach uses Shannon diversity as the
alpha diversity measure and Jensen–Shannon divergence as the beta diversity
measure. The score is mean difference of Shannon diversity between test sample
and all references samples multiplied by the mean JSD of the test sample to all
reference samples. When calculating this score for reference samples, the
sample being used is excluded from calculating means for alpha and beta diversity.
References
Santiago M et al. (2019). Microbiome predictors of dysbiosis and VRE decolonization in patients with recurrent C. difficile infections in a multi-center retrospective study. AIMS Microbiol, 5:1–18.
Examples
data("WirbelJ_2018")
library(phyloseq)
ps <- WirbelJ_2018
# Define controls as reference samples
ref.samples <- sample_names(subset_samples(WirbelJ_2018,
disease == "healthy"))
alpha.beta.dysbiosis <- combinedShannonJSD(ps,
reference_samples = ref.samples)
head(alpha.beta.dysbiosis)
#> ShannonJSDScore study_name subject_id body_site
#> CCMD11006829ST-21-0 0.19887588 WirbelJ_2018 CCMD11006829ST-21-0 stool
#> CCMD12232071ST-21-0 0.07682596 WirbelJ_2018 CCMD12232071ST-21-0 stool
#> CCMD13071240ST-21-0 0.19646724 WirbelJ_2018 CCMD13071240ST-21-0 stool
#> CCMD13934959ST-21-0 0.08587469 WirbelJ_2018 CCMD13934959ST-21-0 stool
#> CCMD14479708ST-21-0 0.09503974 WirbelJ_2018 CCMD14479708ST-21-0 stool
#> CCMD18872694ST-21-0 0.12595852 WirbelJ_2018 CCMD18872694ST-21-0 stool
#> study_condition disease age age_category gender country
#> CCMD11006829ST-21-0 CRC CRC 42 adult female DEU
#> CCMD12232071ST-21-0 CRC CRC 75 senior male DEU
#> CCMD13071240ST-21-0 CRC CRC 66 senior female DEU
#> CCMD13934959ST-21-0 CRC CRC 56 adult male DEU
#> CCMD14479708ST-21-0 CRC CRC 74 senior male DEU
#> CCMD18872694ST-21-0 CRC CRC 63 adult male DEU
#> non_westernized sequencing_platform DNA_extraction_kit
#> CCMD11006829ST-21-0 no IlluminaHiSeq Gnome
#> CCMD12232071ST-21-0 no IlluminaHiSeq Gnome
#> CCMD13071240ST-21-0 no IlluminaHiSeq Gnome
#> CCMD13934959ST-21-0 no IlluminaHiSeq Gnome
#> CCMD14479708ST-21-0 no IlluminaHiSeq Gnome
#> CCMD18872694ST-21-0 no IlluminaHiSeq Gnome
#> PMID number_reads number_bases minimum_read_length
#> CCMD11006829ST-21-0 30936547 83456496 7310970279 45
#> CCMD12232071ST-21-0 30936547 65269931 5370021950 2
#> CCMD13071240ST-21-0 30936547 63427722 5486983593 45
#> CCMD13934959ST-21-0 30936547 36979669 3186342244 45
#> CCMD14479708ST-21-0 30936547 65475493 5637718108 45
#> CCMD18872694ST-21-0 30936547 55300211 4780095276 45
#> median_read_length NCBI_accession curator BMI tnm
#> CCMD11006829ST-21-0 94 <NA> Paolo_Manghi 35 t3n0m0
#> CCMD12232071ST-21-0 88 <NA> Paolo_Manghi 28 t3n2m0
#> CCMD13071240ST-21-0 93 <NA> Paolo_Manghi 23 t3n0m0
#> CCMD13934959ST-21-0 93 <NA> Paolo_Manghi 27 t3n0m0
#> CCMD14479708ST-21-0 92 <NA> Paolo_Manghi 26 t3n0m1
#> CCMD18872694ST-21-0 93 <NA> Paolo_Manghi 25 t3n1m0
#> ajcc nspecies group
#> CCMD11006829ST-21-0 ii 144 case
#> CCMD12232071ST-21-0 iii 110 case
#> CCMD13071240ST-21-0 ii 126 case
#> CCMD13934959ST-21-0 ii 100 case
#> CCMD14479708ST-21-0 iv 110 case
#> CCMD18872694ST-21-0 iii 145 case