README.Rmd

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output: github_document
---

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```{r, include = FALSE}
knitr::opts_chunk$set(
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  fig.path = "man/figures/README-",
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options(tibble.print_min = 5L, tibble.print_max = 5L)
```

# hacksig <img src="man/figures/logo.png" align="right" height="139"/>

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The goal of `hacksig` is to provide a simple and tidy interface to compute single sample scores for gene signatures and methods applied in cancer transcriptomics.

Scores can be obtained either for custom lists of genes or for a manually curated collection of gene signatures, including:

-   [CINSARC](https://doi.org/10.1038/nm.2174);
-   [ESTIMATE](https://doi.org/10.1038/ncomms3612);
-   [Immunophenoscore](https://doi.org/10.1016/j.celrep.2016.12.019);
-   [Cytolitic activity](https://doi.org/10.1016/j.cell.2014.12.033);
-   and more (use `get_sig_info()` to get a complete list of the implemented signatures)

At present, signature scores can be obtained either with the original publication method or using one of three single sample scoring alternatives, namely: *combined z-score*, *single sample GSEA* and *singscore*.

## Installation

You can install the last stable version of hacksig from [CRAN](https://CRAN.R-project.org) with:

```{r, eval=FALSE}
install.packages("hacksig")
```

Or the development version from [GitHub](https://github.com/) with:

```{r, eval=FALSE}
# install.packages("devtools")
devtools::install_github("Acare/hacksig")
```

## Usage

You can learn more about usage of the package in `vignette("hacksig")`.

```{r, message=FALSE}
library(hacksig)
library(dplyr)
library(future)
```

### Available signatures

```{r}
get_sig_info()
```

### Check your signatures

```{r}
check_sig(test_expr, signatures = "estimate")
```

### Compute single sample scores

```{r}
hack_sig(test_expr, signatures = c("ifng", "cinsarc"), method = "zscore")
```

### Stratify your samples

```{r}
test_expr %>% 
    hack_sig("estimate", method = "singscore", direction = "up") %>% 
    stratify_sig(cutoff = "median")
```

### Speed-up computation time

```{r}
plan(multisession)
hack_sig(test_expr, method = "ssgsea")
```

## Contributing

If you have any suggestions about adding new features or signatures to `hacksig`, please create an issue on [GitHub](https://github.com/Acare/hacksig/issues). Gene-level information about gene signatures are stored in `data-raw/hacksig_signatures.csv` and can be used as a template for requests.