rename AG

bio-datascience · Jan 27, 2021 · ad3d0ff · ad3d0ff
1 parent 432759c
commit ad3d0ff
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Showing 3 changed files with 5 additions and 4 deletions.
diff --git a/2_beta_diversity_AG/2.1_beta_diversity.R → 2_beta_diversity_AG/2.1_beta_diversity_AG.R b/2_beta_diversity_AG/2.1_beta_diversity.R → 2_beta_diversity_AG/2.1_beta_diversity_AG.R
diff --git a/3_mean_diff_test_AG/3.1_high_dim_test.R → 3_mean_diff_test_AG/3.1_high_dim_test_AG.R b/3_mean_diff_test_AG/3.1_high_dim_test.R → 3_mean_diff_test_AG/3.1_high_dim_test_AG.R
diff --git a/...abundance_AG/4.1_variance_ref_selection.R → ...ndance_AG/4.1_variance_ref_selection_AG.R b/...abundance_AG/4.1_variance_ref_selection.R → ...ndance_AG/4.1_variance_ref_selection_AG.R
@@ -13,9 +13,6 @@ load('./design_AG/agdata.rda')
 ## load sample/matched_data
 load('./design_AG/dat_matched_smoke_ag.RData')
 
-## load W matrix for randomization test
-load("./design_AG/W_paired_smoke_ag.Rdata")
-
 ############################
 # create a phyloseq object # 
 ############################
@@ -62,9 +59,13 @@ taxa_var_ait <- apply(unname(otu_table(ps_ait)), 1, function(x) var(x))
 
 plot(taxa_prev, taxa_var_ait)
 
-condition <- taxa_var_ait < 3 & taxa_prev > .4
+condition <- taxa_var_ait < 3 & taxa_prev > .5
 condition_ref <- which(condition)
 
+# check if at least one reference taxa is in all samples
+reference_values <- apply(otu_table(ps)[condition_ref,], 2, sum)
+table(reference_values)[1:3]
+
 plot(taxa_prev, taxa_var_ait, col = factor(condition))
 
 # save(condition_ref, file = "./4_differential_abundance_AG/selected_ref_genus_AG.RData")