From 7c010e370699e441ce0956eb2dc444931a13e817 Mon Sep 17 00:00:00 2001 From: Biacordazzo Date: Mon, 10 Feb 2025 14:51:13 -0500 Subject: [PATCH 1/3] fix inconsistency in README --- README.md | 11 +++++------ 1 file changed, 5 insertions(+), 6 deletions(-) diff --git a/README.md b/README.md index f471502..1a31af8 100644 --- a/README.md +++ b/README.md @@ -105,13 +105,12 @@ The input to *FEAST* is composed of two tab-delimited ASCII text files: count matrix (first 4 rows and columns): -| | ERR525698 |ERR525693 | ERR525688| ERR525699| +| | taxa_1 |taxa_2 | taxa_3| taxa_4| | ------------- | ------------- |------------- |------------- |------------- | -| taxa_1 | 0 | 5 | 0|20 | -| taxa_2 | 15 | 5 | 0|0 | -| taxa_3 | 0 | 13 | 200|0 | -| taxa_4 | 4 | 5 | 0|0 | - +| ERR525698 | 0 | 15 | 0| 4 | +| ERR525693 | 5 | 5 | 13 | 5 | +| ERR525688 | 0 | 0 | 200 | 0 | +| ERR525699 | 20 | 0 | 0 | 20 | (2) metadata - An m by 3 table, where m is the number of samples. The metadata table has three columns (i.e., 'Env', 'SourceSink', 'id'). The first column is a description of the sampled environment (e.g., human gut), the second column indicates if this sample is a source or a sink (can take the value 'Source' or 'Sink'). The third column is the Sink-Source id. When using multiple sinks, each tested with the same group of sources, only the rows with 'SourceSink' = Sink will get an id (between 1 - number of sinks in the data). In this scenario, the sources’ ids are blank. When using multiple sinks, each tested with a distinct group of sources, each combination of sink and its corresponding sources should get the same id (between 1 - number of sinks in the data). Note that these names must be respected. From 3b9a9716f01821ae6adba265d2655b36aaf6d9b4 Mon Sep 17 00:00:00 2001 From: Biacordazzo Date: Mon, 10 Feb 2025 14:53:52 -0500 Subject: [PATCH 2/3] match values in table with otu_example.txt --- README.md | 8 ++++---- 1 file changed, 4 insertions(+), 4 deletions(-) diff --git a/README.md b/README.md index 1a31af8..e8443c7 100644 --- a/README.md +++ b/README.md @@ -107,10 +107,10 @@ count matrix (first 4 rows and columns): | | taxa_1 |taxa_2 | taxa_3| taxa_4| | ------------- | ------------- |------------- |------------- |------------- | -| ERR525698 | 0 | 15 | 0| 4 | -| ERR525693 | 5 | 5 | 13 | 5 | -| ERR525688 | 0 | 0 | 200 | 0 | -| ERR525699 | 20 | 0 | 0 | 20 | +| ERR525698 | 0 | 5 | 0| 20 | +| ERR525693 | 15 | 5 | 0 | 0 | +| ERR525688 | 0 | 13 | 200 | 0 | +| ERR525699 | 4 | 5 | 0 | 20 | (2) metadata - An m by 3 table, where m is the number of samples. The metadata table has three columns (i.e., 'Env', 'SourceSink', 'id'). The first column is a description of the sampled environment (e.g., human gut), the second column indicates if this sample is a source or a sink (can take the value 'Source' or 'Sink'). The third column is the Sink-Source id. When using multiple sinks, each tested with the same group of sources, only the rows with 'SourceSink' = Sink will get an id (between 1 - number of sinks in the data). In this scenario, the sources’ ids are blank. When using multiple sinks, each tested with a distinct group of sources, each combination of sink and its corresponding sources should get the same id (between 1 - number of sinks in the data). Note that these names must be respected. From 7707e196cb6ce16d85999535622ef9f65bc1a277 Mon Sep 17 00:00:00 2001 From: Biacordazzo Date: Tue, 11 Feb 2025 12:11:01 -0500 Subject: [PATCH 3/3] change file paths and feast installation from master --- vignettes/FEAST_example.Rmd | 11 ++++------- 1 file changed, 4 insertions(+), 7 deletions(-) diff --git a/vignettes/FEAST_example.Rmd b/vignettes/FEAST_example.Rmd index 2c8fa13..4cc9c35 100644 --- a/vignettes/FEAST_example.Rmd +++ b/vignettes/FEAST_example.Rmd @@ -32,14 +32,11 @@ lapply(Packages, library, character.only = TRUE) install *FEAST* using devtools ```{r install_FEAST, echo=T, results='hide', message=F, warning=F} -devtools::install_github("cozygene/FEAST", ref = "FEAST_beta") +#devtools::install_github("cozygene/FEAST") ``` - - ```{r load, echo=T, results='hide', message=F, warning=F} library(FEAST) - ``` ## Input Format @@ -53,8 +50,8 @@ The input to *FEAST* is composed of two tab-separated ASCII text files : Load the datasets as follows: ```{r example_input} -metadata <- Load_metadata(metadata_path = "~/FEAST/Data_files/metadata_example_multi.txt") -otus <- Load_CountMatrix(CountMatrix_path = "~/FEAST/Data_files/otu_example_multi.txt") +metadata <- Load_metadata(metadata_path = "../../FEAST/Data_files/metadata_example_multi.txt") +otus <- Load_CountMatrix(CountMatrix_path = "../../FEAST/Data_files/otu_example_multi.txt") ``` @@ -73,7 +70,7 @@ As input, *FEAST* takes mandatory arguments: Run FEAST, saving the output with prefix "demo". ```{r analyze_example} -FEAST_output <- FEAST(C = otus, metadata = metadata, different_sources_flag = 1, dir_path = "~/FEAST/Data_files/", +FEAST_output <- FEAST(C = otus, metadata = metadata, different_sources_flag = 1, dir_path = "../../FEAST/Data_files/", outfile="demo") ```