Dear All @sagunmaharjann,
I am working on testing a newly developed tool to study the microbial co-occurrence and I need a simulation datasets with ground truth to test the performance of our method compared to other standardized methods like MDINE, SPIEC-EASY.
Luckily I found SparseDOSSA R package and I tried it myself.
library(sparseDOSSA)
n.microbes <- 200
n.samples <- 100
n.metadata <- 2
sparseDOSSA::sparseDOSSA( number_features = n.microbes,
number_samples = n.samples,
number_metadata = n.metadata,
runBugBug = TRUE, bugBugCorr = “0.2”,
bugs_to_spike = 5 )
And I got the output as described in the tutorial. I have attached my output. SyntheticMicrobiome-Counts.csv (415.9 KB)
I would like to know where can I get the ground truth of the co-occurence pattern? And also, in the SyntheticMicrobiome-Counts files, there are different labels.
Feature_Lognormal_1: Rows with these kind of label represents the counts
What does the following label means? (a_5, d_1_1)?
Feature_BugToBugAssociations_a_5_d_1_1
And I also would like to know which sets of rows I should use for testing the tools?
|Feature_BugToBugAssociations_a_5_d_1_1|0|0.004555809|0.023195876|0.040849673|0.022082019|0|
|---|---|---|---|---|---|---|
|Feature_BugToBugAssociations_a_5_d_1_2|0|0|0|0|0|0|
|Feature_BugToBugAssociations_a_5_d_1_3|0.004207574|0|0|0|0|0|
|Feature_BugToBugAssociations_a_5_d_1_4|0|0|0|0|0|0.001295337|
|Feature_BugToBugAssociations_a_5_d_1_5|0|0|0.065721649|0|0.013669821|0.050518135|
|Feature_BugToBugAssociations_a_5_d_1_6|0|0|0|0|0|0.005181347|
|Feature_BugToBugAssociations_a_5_d_1_7|0|0.006833713|0.018041237|0|0.004206099|0|
|Feature_BugToBugAssociations_a_5_d_1_8|0|0|0|0|0|0|
|Feature_BugToBugAssociations_a_5_d_1_9|0|0|0|0|0|0|
|Feature_BugToBugAssociations_a_5_d_1_10|0|0|0|0|0|0|
|Feature_BugToBugAssociations_a_5_d_1_11|0.001402525|0|0|0|0|0|
|Feature_BugToBugAssociations_a_5_d_1_12|0|0|0.00257732|0|0.015772871|0.019430052|
|Feature_BugToBugAssociations_a_5_d_1_13|0|0.043280182|0|0.011437908|0|0.001295337|
|Feature_BugToBugAssociations_a_5_d_1_14|0|0|0|0|0|0|