Commit version 1.0.0 of EPIC.

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+^data-raw$
+^README\.Rmd$
+^README-.*\.png$

.gitignore

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+# Hidden files automatically created by mac os or autosaved from
+#  some other program
+.DS_Store
+._*
+*~
+~$*
+
+# R-files and data/directories not to keep
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+.Rapp.history
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+temp*.R
+inst/doc
+data-raw

DESCRIPTION

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+Package: EPIC
+Type: Package
+Title: Estimate the Proportion of Immune and Cancer cells
+Version: 1.0.0
+Authors@R: as.person(c(
+  "Julien Racle <[email protected]> [aut, cre]",
+  "David Gfeller <[email protected]> [aut]"
+  ))
+Description: Package implementing EPIC method to estimate the proportion of
+    immune and cancer cells from bulk gene expression data. It is based on
+    reference gene expression profiles for the main immune cell types and it
+    predicts the proportion of these cells and of the remaining "other cells"
+    that are the remaining cells (cancer, stromal, endothelial) for which no
+    reference profile is given.
+Depends: R (>= 3.2.0)
+License: file LICENSE
+LazyData: TRUE
+RoxygenNote: 5.0.1
+Suggests: testthat,
+    knitr,
+    rmarkdown
+Imports: stats
+VignetteBuilder: knitr

LICENSE

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+SOFTWARE LICENSE AGREEMENTFOR ACADEMIC NON-COMMERCIAL RESEARCH PURPOSES ONLYThis Agreement is made between Ludwig Institute for Cancer Research Ltd, a not-for-profit organization with its registered office at Stadelhoferstrasse 22, 8001 Zurich, Switzerland, and having a place of business at 666 Third Avenue, New York, NY 10017,USA (“LICR”) and the  (“LICENSEE”)  and is effective at the date the downloading is completed (“EFFECTIVE DATE”).WHEREAS, LICENSEE desires to license the PROGRAM, as defined hereinafter, and LICR wishes to have this PROGRAM utilized in the public interest, subject only to the royalty-free, nonexclusive, nontransferable license; andWHEREAS, LICENSEE desires to license the PROGRAM and LICR desires to grant a license on the following terms and conditions.NOW, THEREFORE, in consideration of the promises and covenants made herein, the parties hereto agree as follows:1. DEFINITIONS1.1 PROGRAM shall mean the source code known as EPIC (version 1.0), as it exists on the EFFECTIVE DATE.2. LICENSE2.1 Grant. Subject to the terms of this Agreement, LICR hereby grants to LICENSEE, solely for academic non-commercial research purposes, a non-exclusive, non-transferable license to: (a) download, execute and display the PROGRAM and (b) create bug fixes and modify the PROGRAM. LICENSEE hereby automatically grants to LICR a non-exclusive, royalty-free, irrevocable license to any LICENSEE bug fixes or modifications to the PROGRAM with unlimited rights to sublicense and/or distribute.  LICENSEE agrees to provide any such modifications and bug fixes to LICR promptly upon their creation.The LICENSEE may apply the PROGRAM in a pipeline to data owned by users other than the LICENSEE and provide these users the results of the PROGRAM provided LICENSEE does so for academic non-commercial purposes only. 2.2 No Sublicensing or Additional Rights. LICENSEE shall not sublicense or distribute the PROGRAM, in whole or in part, without prior written permission from LICR. LICENSEE shall ensure that all of its users agree to the terms of this Agreement. LICENSEE further agrees that it shall not put the PROGRAM on a network, server, or other similar technology that may be accessed by anyone other than the LICENSEE and its employees and users who have agreed to the terms of this Agreement.2.3 License Limitations. Nothing in this Agreement shall be construed to confer any rights upon LICENSEE by implication, estoppel, or otherwise to any computer software, trademark, intellectual property, or patent rights of LICR, or of any other entity, except as expressly granted herein. LICENSEE agrees that the PROGRAM, in whole or part, shall not be used for any commercial purpose, including without limitation, as the basis of a commercial software or hardware product or to provide services. LICENSEE further agrees that the PROGRAM shall not be copied or otherwise adapted in order to circumvent the need for obtaining a license for use of the PROGRAM.3. OWNERSHIP OF INTELLECTUAL PROPERTYLICENSEE acknowledges that title to the PROGRAM shall remain with LICR. The PROGRAM shall be marked with the notice of attribution to contributors. LICENSEE shall retain such notice on all copies. LICENSEE agrees to include appropriate attribution if any results obtained from use of the PROGRAM are included in any publication.Notice of attribution: The EPIC (version 1.0) program was made available through the generosity of Ludwig Institute for Cancer Research Ltd.LICENSEE shall not use any trademark or trade name of LICR, or any variation, adaptation, or abbreviation, of such marks or trade names, or any names of officers, faculty, students, employees, or agents of LICR except as states above for attribution purposes.4. 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LICR MAKES NO REPRESENTATIONS OR WARRANTIES OF ANY KIND CONCERNING THE PROGRAM, EXPRESS OR IMPLIED, INCLUDING, WITHOUT LIMITATION, WARRANTIES OF MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE, NONINFRINGEMENT, OR THE ABSENCE OF LATENT OR OTHER DEFECTS, WHETHER OR NOT DISCOVERABLE. LICR EXTENDS NO WARRANTIES OF ANY KIND AS TO PROGRAM CONFORMITY WITH WHATEVER USER MANUALS OR OTHER LITERATURE MAY BE ISSUED FROM TIME TO TIME.IN NO EVENT SHALL LICR OR ITS RESPECTIVE DIRECTORS, OFFICERS, EMPLOYEES, AFFILIATED INVESTIGATORS AND AFFILIATES BE LIABLE FOR INCIDENTAL OR CONSEQUENTIAL DAMAGES OF ANY KIND, INCLUDING, WITHOUT LIMITATION, ECONOMIC DAMAGES OR INJURY TO PROPERTY AND LOST PROFITS, REGARDLESS OF WHETHER LICR SHALL BE ADVISED, SHALL HAVE OTHER REASON TO KNOW, OR IN FACT SHALL KNOW OF THE POSSIBILITY OF THE FOREGOING.6. ASSIGNMENTThis Agreement is personal to LICENSEE and any rights or obligations assigned by LICENSEE without the prior written consent of LICR shall be null and void.7. 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All notices under this Agreement shall be deemed effective upon receipt.7.4 Amendment and Waiver; Entire Agreement. This Agreement may be amended, supplemented, or otherwise modified only by means of a written instrument signed by all parties. Any waiver of any rights or failure to act in a specific instance shall relate only to such instance and shall not be construed as an agreement to waive any rights or fail to act in any other instance, whether or not similar. This Agreement constitutes the entire agreement among the parties with respect to its subject matter and supersedes prior agreements or understandings between the parties relating to its subject matter.7.5 Binding Effect; Headings. This Agreement shall be binding upon and inure to the benefit of the parties and their respective permitted successors and assigns. All headings are for convenience only and shall not affect the meaning of any provision of this Agreement.7.6 Governing Law. This Agreement is governed by the laws of Switzerland and the Canton of Vaud.

NAMESPACE

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+# Generated by roxygen2: do not edit by hand
+
+export(EPIC)

NEWS

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+Version 1.0.0
+------------------------------------------------------------------------
+* Public release of EPIC package.

R/EPIC_descr.R

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+#' EPIC: a package to Estimate the Proportion of Immune and Cancer cells from
+#'  tumor gene expression data.
+#'
+#' EPIC package provides the function and immune cell reference profiles to
+#' estimate the proportion of immune and other cells from bulk gene expression
+#' data.
+#'
+#' @section EPIC functions:
+#' \code{\link{EPIC}} is the main function to call to estimate the
+#'  various cells proportions from a bulk sample.
+#'
+#' @section Included datasets:
+#' \code{\link{BRef}}, \code{\link{BRef.tpm}}: reference profiles from
+#'    circulating immune cells.
+#'
+#'  \code{\link{TRef.tpm}}: reference profiles from immune cells obtained
+#'  from single cell data of tumor infiltrating cells from melanoma patients.
+#'
+#' \code{\link{hoek_data}}: example dataset containing data from Hoek et al,
+#'  2015, PLoS One.
+#'
+#' \code{\link{mRNA_cell_default}}: values of mRNA per cell for the main cell
+#'  types.
+#'
+#' @section Authors:
+#' Julien Racle <\email{[email protected]}> and David Gfeller <\email{
+#'  [email protected]}>.
+#'
+#' @docType package
+#' @name EPIC.package
+NULL
+
+
+#' Reference profiles from circulating immune cells.
+#'
+#' A dataset containing the reference profiles obtained from immune cell
+#' samples of \emph{B-}, \emph{NK-}, \emph{T-cells}, \emph{Monocytes}
+#' and \emph{Neutrophils} purified from PBMC or whole blood.
+#'
+#' The original samples were obtained from healthy donors and donors after
+#' influenza vaccination or with diabetes, sepsis or multiple sclerosis.
+#'
+#' @section Similar datasets:
+#'  \code{BRef} (main reference profiles, using data from sources 1-3 below)
+#'
+#'
+#' @format A list of 3 elements: \describe{ \item{$refProfiles,
+#'   $refProfiles.var}{Matrices (nGenes x nRefCells) of the normalized gene
+#'   expression from the reference cells and the variability of this gene
+#'   expression for each gene and each cell type} \item{$sigGenes}{A list of 100
+#'   signature genes used to deconvolve the cell proportions} }
+#'
+#' @source \enumerate{
+#'  \item \url{https://www.ebi.ac.uk/arrayexpress/experiments/E-GEOD-64655},
+#'  \item \url{https://www.ebi.ac.uk/arrayexpress/experiments/E-GEOD-60424/},
+#'  \item \url{http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE51984}
+#'  }
+"BRef"
+
+#' @section Similar datasets:
+#' \code{BRef.tpm} (reference profiles based on same data as \code{BRef},
+#'  but given in TPM counts instead of raw counts)
+#' @rdname BRef
+"BRef.tpm"
+
+#' Reference profiles obtained from single cell data of tumor infiltrating
+#' cells.
+#'
+#' A dataset containing the reference profiles given in TPM from various cell
+#' types: \emph{B-}, \emph{NK-}, \emph{T-cells} and \emph{Macrophages}.
+#'
+#' These were obtained from single-cell RNA-seq data from 9 donors from
+#' the publication of Tirosh et al., 2016, Science. The samples
+#' come from cancer metastases of melanoma (extracted from primary tumors
+#' and non-lymphoid tissue metastases). The classification for each sample with
+#' respect to each cell type is the one given by Tirosh et al.
+#'
+#' @format A list of 3 elements: \describe{ \item{$refProfiles,
+#'   $refProfiles.var}{Matrices (nGenes x nRefCells) of the normalized gene
+#'   expression from the reference cells and the variability of this gene
+#'   expression for each gene and each cell type} \item{$sigGenes}{A list of 80
+#'   signature genes used to deconvolve the cell proportions} }
+#'
+#' @source \url{http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE72056}
+"TRef.tpm"
+
+#' Values of mRNA / cell for the main cell types.
+#'
+#' These values have been obtained from experiments (see \cite{EPIC} publication).
+#' For the other uncharacterized cells, we use a value of 0.4 as described
+#' in \cite{EPIC} publication. For macrophages we don't have specific values but
+#' assumed here it is the same value as for monocytes.
+#'
+#' @format A named numeric vector of the relative amount of mRNA per cell type.
+#'  There are two additional "special cell types": the \emph{otherCells} which
+#'  correspond to the uncharacterized cells present in the sample but without
+#'  any reference profile and the \emph{default} which is the default value used
+#'  for cells with reference profiles but without a value specified in the
+#'  \code{mRNA_cell_default} vector.
+"mRNA_cell_default"
+
+#' Example dataset containing data from Hoek et al, 2015, PLoS One.
+#'
+#' This dataset contains a subset of the full Hoek et al data. It contains only
+#' the data from the two healthy donors PBMC before influenza vaccination.
+#'
+#' @format This is a list of 3 elements: \describe{
+#'  \item{$rawCounts}{(matrix of 51574 genes x 2 donors) The raw read counts
+#'    from the two donors. It has been obtained by mapping the original
+#'    fastq files to \emph{hg19} genome with help of \emph{tophat} and
+#'    \emph{htseq-count}.}
+#'  \item{$cellFractions.obs}{(matrix of 2 donors x 6 cell types) The
+#'    proportions of the different immune cells in the PBMC from the 2 donors,
+#'    as measured by FACS by Hoek et al.}
+#'  \item{$cellFractions.pred}{(matrix of 2 donors x 7 cell types) The
+#'    proportions of the different immune cells and of a potential additional
+#'    uncharacterized cell, as predicted by EPIC based on the rawCounts and
+#'    the profiles \code{reference=BRef}.}
+#' }
+#'
+#' @source The description of this data can be found here:
+#'  \href{http://dx.doi.org/10.1371/journal.pone.0118528}{link to paper}
+#'  and \href{https://www.ebi.ac.uk/arrayexpress/experiments/E-GEOD-64655}{link
+#'  to data}.
+"hoek_data"
+