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jjmpal · Jan 8, 2020 · 00143c5 · 00143c5
1 parent 197da2a
commit 00143c5
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Showing 2 changed files with 23 additions and 14 deletions.
diff --git a/articletwo-rrbiome.R b/articletwo-rrbiome.R
@@ -53,7 +53,7 @@ filter.phenotype.data <- function(pseq,
                       PULSEPRESSURE = myscale(PULSEPRESSURE),
                       MAP = myscale(MAP),
                       SEX = as.factor(SEX),
-                      Q57X = as.factor(Q57X),
+                      Q57X = factor(Q57X, ordered = FALSE),
                       BL_USE_RX_C03 = as.factor(BL_USE_RX_C03),
                       BL_USE_RX_C07 = as.factor(BL_USE_RX_C07),
                       BL_USE_RX_C08 = as.factor(BL_USE_RX_C08),
@@ -379,3 +379,9 @@ deseq.list <- function(var.CL, var.CL.min) {
     })
     l[!duplicated(l)]
 }
+
+coretaxa <- function(pseq, detection = 0.1/100, prevalence = 1/100) {
+    microbiome::transform(pseq, "compositional") %>%
+        core(detection = detection, prevalence = prevalence) %>%
+        taxa
+}
diff --git a/articletwo.Rmd b/articletwo.Rmd
@@ -122,26 +122,20 @@ names.dset <- getdescriptions()
 eLoading phyloseq object
 
 ```{r data
-pseq.genus <- import_filter_data("data/phfinrisk_genus_all_drop50k_2018-11-16.RDs")
 pseq.species <- import_filter_data("data/phfinrisk_species_all_drop50k_2018-12-21.RDs")
+pseq.genus <- import_filter_data("data/phfinrisk_genus_all_drop50k_2018-11-16.RDs")
+pseq.genus.coretaxa <- coretaxa(pseq.genus, detection = 0.1/100, prevalence = 1/100)
 ```
 
 Species has average number of reads `r pseq.species %>% sample_sums %>% mean` and
-genus `r pseq.genus %>% sample_sums %>% mean`.
+genus `r pseq.genus %>% sample_sums %>% mean`. Core has length 
+`r length(pseq.genus.coretaxa)`.
 
 At species level meta has dimensions (`r dim(meta(pseq.species))`) and
 there ntaxa is `r ntaxa(pseq.species)`. At genus level meta has
 dimensions (`r dim(meta(pseq.genus))`) and there ntaxa is 
 `r ntaxa(pseq.genus)`. 
 
-```{r defining genus core}
-pseq.genus.core <- microbiome::transform(pseq.genus, "compositional") %>%
-    core(detection = 0.1/100, prevalence = 1/100)
-```
-
-At genus-core level meta has dimensions (`r dim(meta(pseq.genus.core))`) 
-and there ntaxa is `r ntaxa(pseq.genus.core)`.
-
 ## Variables
 
 ```{r my variables}
@@ -153,6 +147,8 @@ var.CL <- c("BL_AGE", "SEX", "BMI", "CURR_SMOKE", "Q57X", "PREVAL_DIAB",
 
 ## MODELS
 
+### Bray curtis distance matrix
+
 ```{r matrix calculation}
 if (!file.exists("rds/bray.dist.m.species.rds")) {
     bray.dist.m.species <- calculate.beta.matrix(pseq.species)
@@ -162,6 +158,8 @@ if (!file.exists("rds/bray.dist.m.species.rds")) {
 }
 ```
 
+### Beta diversity
+
  ```{r adonis calculation}
  if (!file.exists("rds/adonis.species.rds")) {
      adonis.species <- calculate.betadiversity(pseq = pseq.species,
@@ -175,6 +173,8 @@ if (!file.exists("rds/bray.dist.m.species.rds")) {
  }
 ```
 
+### PCoA
+
 ```{r pcoa calculate}
 if (!file.exists("rds/pcoa.ordinate.rds")) {
     pcoa.abundances <- microbiome::transform(pseq.species, 'compositional')
@@ -185,17 +185,20 @@ if (!file.exists("rds/pcoa.ordinate.rds")) {
 }
 ```
 
+### DeSeq2
+
 ```{r deseq2}
 if (!file.exists("rds/dds.rds")) {
-    pseq.genus.core.deseq <-  prune_taxa(taxa(pseq.genus.core), pseq.genus)
+    pseq.genus.core.deseq <-  prune_taxa(pseq.genus.coretaxa, pseq.genus)
     
     dds <- lapply(c2l(var.BP), function(x) {
         dds.data <- phyloseq_to_deseq2(pseq.genus.core.deseq, deseq.formula(x, var.CL))
         DESeq(dds.data,
               test="Wald",
               fitType="parametric",
               parallel = TRUE,
-              BPPARAM=MulticoreParam(16))})
+              BPPARAM=MulticoreParam(16))
+    })
 
     saveRDS(dds, file = "rds/dds.rds")
 } else {
@@ -205,7 +208,7 @@ if (!file.exists("rds/dds.rds")) {
 
 ```{r comparing deseq2}
 if (!file.exists("rds/dds3.rds")) {
-    pseq.genus.core.deseq <-  prune_taxa(taxa(pseq.genus.core), pseq.genus)
+    pseq.genus.core.deseq <-  prune_taxa(pseq.genus.coretaxa, pseq.genus)
     dds3 <- lapply(deseq.list(var.CL, var.CL.min), function(x, dds) {
         dds.data <- phyloseq_to_deseq2(dds, deseq.formula(x, "HYPERTENSION"))
         DESeq(dds.data,