Skip to content

Commit

Permalink
updated readme
Browse files Browse the repository at this point in the history
  • Loading branch information
@michbur
michbur committed Jul 17, 2024
1 parent 718a497 commit d21f176
Show file tree
Hide file tree
Showing 2 changed files with 41 additions and 27 deletions.
7 changes: 7 additions & 0 deletions README.Rmd
View file
Original file line number Diff line number Diff line change
Expand Up @@ -34,6 +34,13 @@ Our package provides fast and efficient generation of synthetic k-mer datasets w
- additive impact of custom interactions (logical expressions using motifs).


To learn more, please visit: https://biogenies.info/kmerFilters/

Specific resources:

- [Simulation description](https://biogenies.info/kmerFilters/articles/simulation_description.html)


## How to install

You can install the latest version from GitHub:
Expand Down
61 changes: 34 additions & 27 deletions README.md
View file
Original file line number Diff line number Diff line change
Expand Up @@ -32,6 +32,13 @@ on few biological cases, such as
- additive impact of custom interactions (logical expressions using
motifs).

To learn more, please visit: <https://biogenies.info/kmerFilters/>

Specific resources:

- [Simulation
description](https://biogenies.info/kmerFilters/articles/simulation_description.html)

## How to install

You can install the latest version from GitHub:
Expand Down Expand Up @@ -60,16 +67,16 @@ motifs <- generate_motifs(alphabet = alph,

motifs
#> [[1]]
#> [1] "c" "_" "_" "_" "_" "_" "_" "c"
#> [1] "a" "_" "_" "_" "_" "_" "a" "a"
#>
#> [[2]]
#> [1] "b" "_" "_" "_" "d" "_" "_" "b"
#> [1] "d" "a" "_" "a"
#>
#> [[3]]
#> [1] "d" "_" "_" "_" "_" "_" "d"
#> [1] "b" "_" "_" "_" "_" "d"
#>
#> [[4]]
#> [1] "d" "_" "_" "_" "d" "c"
#> [1] "a" "b" "b" "a"
```

Using simulated motifs we can simulate positive and negative sequences
Expand All @@ -82,31 +89,31 @@ results <- generate_kmer_data(n_seq = 20,
motifs = motifs,
n_injections = 4)
results
#> 20 x 14668 sparse Matrix of class "dgCMatrix"
#> 20 x 15154 sparse Matrix of class "dgCMatrix"
#> [[ suppressing 33 column names 'a', 'd', 'b' ... ]]
#>
#> [1,] 1 1 1 1 1 1 1 1 1 1 1 1 1 1 . . . . . . 1 1 1 1 1 1 1 1 1 . . . . ......
#> [2,] 1 1 1 1 1 1 . 1 . 1 1 1 1 1 1 1 1 . . . 1 . 1 1 . 1 1 1 . 1 1 1 1 ......
#> [3,] . 1 1 1 1 . 1 1 1 . 1 . 1 1 . 1 1 . . . 1 . 1 1 1 . . 1 1 . . . 1 ......
#> [4,] 1 1 1 1 1 . 1 1 1 1 1 1 1 1 . 1 1 . . . 1 . 1 1 1 1 1 1 . 1 . 1 . ......
#> [5,] 1 1 1 1 1 . 1 1 1 1 . 1 1 1 . 1 1 . . . 1 1 1 1 1 1 . 1 . . . . . ......
#> [6,] 1 1 1 1 1 1 1 1 . . 1 . 1 . . 1 . 1 1 1 1 . . 1 1 1 1 1 1 1 . . 1 ......
#> [7,] 1 1 1 1 1 1 . 1 . 1 1 1 1 . 1 1 . . . 1 1 1 . 1 1 . 1 1 1 . 1 . 1 ......
#> [8,] 1 1 1 1 1 . 1 1 1 . . . 1 1 . . 1 1 . 1 1 . 1 1 1 1 1 1 1 . 1 . . ......
#> [9,] 1 1 1 1 1 1 1 1 1 1 1 . 1 1 . 1 . 1 . 1 . 1 1 1 . 1 1 1 1 . 1 . 1 ......
#> [10,] 1 1 1 1 1 . 1 1 1 . 1 1 1 1 1 1 . 1 1 1 1 1 1 1 1 1 1 1 . 1 1 1 1 ......
#> [11,] 1 1 1 1 1 1 1 1 . . . 1 1 1 1 1 . 1 1 1 1 1 1 1 1 1 1 . 1 1 1 . 1 ......
#> [12,] 1 1 1 1 . 1 1 1 . 1 . 1 1 1 1 1 1 1 . 1 1 . 1 . 1 . 1 1 1 1 . 1 1 ......
#> [13,] 1 1 1 1 1 1 1 . 1 1 1 1 1 . . 1 1 1 1 1 1 . 1 . . 1 1 1 1 . 1 1 1 ......
#> [14,] 1 1 1 1 1 1 1 1 1 1 . . 1 . . . 1 1 1 1 1 1 1 1 . . 1 1 . . . 1 1 ......
#> [15,] 1 1 1 1 1 1 . 1 1 1 . 1 1 1 1 . . 1 1 1 1 1 1 1 1 1 1 1 . 1 1 . . ......
#> [16,] 1 1 1 1 . 1 . . 1 1 . 1 . 1 1 . 1 1 1 1 . 1 1 . . 1 1 1 1 1 . 1 . ......
#> [17,] 1 1 1 1 . 1 1 1 1 1 . . . 1 1 1 1 1 . 1 1 1 1 . 1 1 . . 1 1 . 1 1 ......
#> [18,] 1 1 1 1 1 . 1 . . 1 1 . 1 1 . 1 1 1 . 1 . . 1 . 1 1 1 . 1 1 1 . 1 ......
#> [19,] 1 1 1 1 . . 1 . . . 1 1 1 1 1 1 1 1 1 1 1 1 . . 1 1 1 1 1 1 1 . 1 ......
#> [20,] 1 1 1 1 1 . 1 1 1 . 1 . 1 . . 1 1 1 . 1 . 1 1 1 1 1 1 1 1 . . . 1 ......
#> [1,] 1 1 1 1 1 1 1 1 1 1 1 1 1 1 . . . . . . 1 1 1 1 1 1 1 1 . . . . . ......
#> [2,] 1 1 1 1 . 1 1 1 . 1 1 . 1 1 1 1 1 1 . . 1 1 1 1 1 1 1 1 1 1 1 1 . ......
#> [3,] 1 1 1 1 . 1 1 1 1 1 1 . 1 1 1 1 1 . 1 1 1 . 1 . . 1 1 1 1 1 1 . 1 ......
#> [4,] 1 1 1 1 . 1 1 . 1 1 1 1 . 1 . 1 1 1 . . . . 1 . . . 1 1 1 . 1 1 . ......
#> [5,] 1 1 1 1 . 1 1 1 1 1 . 1 1 1 . . 1 . 1 . . 1 . . . 1 1 1 1 . 1 . 1 ......
#> [6,] 1 1 1 1 . 1 1 1 1 1 1 1 . 1 1 1 1 . 1 . 1 1 . 1 1 . 1 1 1 1 1 1 . ......
#> [7,] 1 1 1 1 1 1 . . 1 . 1 1 1 1 1 1 1 . . 1 . 1 1 . 1 1 1 1 1 . . . . ......
#> [8,] 1 1 1 1 1 1 1 1 1 1 1 1 1 1 . . 1 . . . 1 1 . 1 1 . 1 1 1 1 1 . 1 ......
#> [9,] 1 1 1 1 1 . 1 1 1 1 . . . . 1 1 1 1 1 1 1 1 . . . 1 . . 1 1 1 1 . ......
#> [10,] 1 1 1 1 1 . 1 1 1 1 1 1 1 . 1 1 1 . . 1 1 . 1 . 1 . 1 1 1 1 1 1 1 ......
#> [11,] 1 1 1 1 1 1 . . 1 1 1 1 1 1 1 . . 1 1 . . 1 1 1 1 1 1 . 1 1 . 1 1 ......
#> [12,] 1 1 1 1 . 1 1 1 1 . 1 1 . 1 1 1 1 1 1 1 . . 1 1 1 1 1 1 . . . 1 1 ......
#> [13,] 1 1 1 1 1 . . . 1 . . 1 1 1 1 1 1 1 1 1 1 1 . 1 1 1 . 1 . 1 . 1 1 ......
#> [14,] 1 1 1 1 1 1 1 1 . 1 1 . . . . 1 1 1 1 1 . 1 1 1 1 1 1 1 1 1 . 1 . ......
#> [15,] 1 1 1 1 1 1 1 . 1 1 . 1 . 1 . . . 1 1 1 1 . 1 . 1 1 1 . 1 . 1 . 1 ......
#> [16,] 1 1 1 1 1 1 1 . 1 . 1 . 1 1 . 1 . . 1 1 1 . 1 1 1 1 1 . . . 1 . 1 ......
#> [17,] 1 1 1 1 1 1 . 1 . 1 1 1 . . 1 . 1 1 1 . . 1 1 1 1 1 1 . 1 1 1 1 . ......
#> [18,] 1 1 1 1 1 1 1 1 1 . 1 1 . 1 . . 1 1 1 . 1 1 1 . . 1 . 1 1 1 1 . . ......
#> [19,] 1 1 1 1 1 . 1 1 1 1 1 1 1 . 1 . 1 . 1 . . 1 1 1 1 . 1 . 1 1 1 1 1 ......
#> [20,] 1 1 1 1 . 1 . 1 1 . . 1 1 1 1 1 . . . 1 1 1 1 . 1 1 1 . . . . . 1 ......
#>
#> .....suppressing 14635 columns in show(); maybe adjust 'options(max.print= *, width = *)'
#> .....suppressing 15121 columns in show(); maybe adjust 'options(max.print= *, width = *)'
#> ..............................
```

Expand All @@ -121,7 +128,7 @@ For example, the following code:

``` r
get_target_additive(results)
#> [1] 1 1 0 1 0 0 1 0 1 1 0 0 0 0 0 1 0 0 0 0
#> [1] 1 1 0 1 1 1 0 0 0 1 0 0 0 0 0 0 0 0 0 0
```

creates a binary response variable based on the logistic regression
Expand Down

0 comments on commit d21f176

Please sign in to comment.