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README and old feast version #68

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7c010e3
fix inconsistency in README
Biacordazzo Feb 10, 2025
3b9a971
match values in table with otu_example.txt
Biacordazzo Feb 10, 2025
7707e19
change file paths and feast installation from master
Biacordazzo Feb 11, 2025
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11 changes: 5 additions & 6 deletions README.md
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Original file line number Diff line number Diff line change
Expand Up @@ -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 | 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.
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11 changes: 4 additions & 7 deletions vignettes/FEAST_example.Rmd
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Expand Up @@ -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
Expand All @@ -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")
```


Expand All @@ -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")

```
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