Commit 2b597ffa authored by domingue's avatar domingue
Browse files

Major change: new name.

parent 54553d50
^coReSCF\.Rproj$
^corescf\.Rproj$
^\.Rproj\.user$
^LICENSE\.md$
^doc$
......
......@@ -8,7 +8,7 @@ getOption("repos")
devtools::load_all(".")
install_package("biomaRt")
devtools::load_all(".")
source('~/Documents/coReSCF/R/zzz.R')
source('~/Documents/corescf/R/zzz.R')
op <- options()
op
devtools::load_all(".")
......
Package: coReSCF
Package: corescf
Title: Collection of Useful CSF Functions
Description: Collection of useful custom functions as part of the CSF workflows.
Version: 0.4.0.0000
Version: 0.5.0.0000
Authors@R: c(
person(given = "António",
family = "Domingues",
......
......@@ -49,7 +49,7 @@ first_group <- function(x, which = 1) {
#' Convert a named vector to a data frame
#'
#' Deprecated, use [coReSCF::vec_as_df()] instead.
#' Deprecated, use [corescf::vec_as_df()] instead.
#'
#' @param namedVec Named vector
#'
......@@ -63,7 +63,7 @@ first_group <- function(x, which = 1) {
#' vec2df(1:3)
#' }
vec2df <- function(namedVec) {
.Deprecated("coReSCF::vec_as_df")
.Deprecated("corescf::vec_as_df")
namedVec %>% {
data.frame(name = names(.), value = ., row.names = NULL)
}
......@@ -252,7 +252,7 @@ pretty_names <- function(some_names, make_unique = FALSE) {
#' Clean up colnames
#'
#' Removes funky characters from colnames, and converts to lower case, to make them suitable for computational work
#' Uses [coReSCF::pretty_names()]
#' Uses [corescf::pretty_names()]
#'
#' @param df a data.frame
#'
......
......@@ -37,7 +37,7 @@ filterByExpression <- function(fpkmMat, minFPKM = 1, logMode = F) {
#' Filter expressed genes
#'
#' Wrapper for [cummeRbund::repFpkmMatrix()] and [coReSCF::filterByExpression()]
#' Wrapper for [cummeRbund::repFpkmMatrix()] and [corescf::filterByExpression()]
#'
#' @note cummeRbund is now very old and has been superseded by better tools. It should no be the first choice for analysis.
#'
......@@ -60,11 +60,11 @@ getExpressedGenes <- function(cuff, ...) {
#' Keep expressed genes
#'
#' #' Deprecated, use [coReSCF::filter_expressed_genes()] instead.
#' #' Deprecated, use [corescf::filter_expressed_genes()] instead.
#'
#' @param df data.frame with expression values and column with gene IDs
#' @param id_col the column with gene identifiers. Default ensembl_gene_id
#' @param ... Arguments to be passed to [coReSCF::filterByExpression()]
#' @param ... Arguments to be passed to [corescf::filterByExpression()]
#'
#' @export
#'
......@@ -280,7 +280,7 @@ getGeneInfo <- function(gene_ids) {
#' Subset hits
#'
#' Extract hits from the table of DGE. Assumes the output format from the coreSCF DGE workflow.
#' Extract hits from the table of DGE. Assumes the output format from the corescf DGE workflow.
#'
#' @param deData Table of differential expressed genes
#' @param s1 Condition 1
......@@ -391,12 +391,12 @@ s1_eq_s2 <- function(deData, sample_1, sample_2, gene_background = all_genes) {
#' Intersect genes
#'
#' Intersect multiple list of differentially expressed genes.
#' @note Assumes the output format from the coreSCF DGE workflow. Table with multiple conditions
#' @note Assumes the output format from the corescf DGE workflow. Table with multiple conditions
#'
#' @param deData <what param does>
#' @param sample_1 Condition of interest
#' @param sample_two Conditions to intersect with
#' @param .intersect_method Which function to use for the intersection? Example [coReSCF::s1_gt_s2()]
#' @param .intersect_method Which function to use for the intersection? Example [corescf::s1_gt_s2()]
#' @param ... Other methods passed to the intersection function
#'
#' @return a data.frame
......
......@@ -14,9 +14,10 @@ devtools::install_git(
credentials = NULL,
dependencies = TRUE
)
library("corescf")
```
install
assuming the ssh keys are added to gitlab.
install assuming the ssh keys are added to gitlab.
If you run into problems, in OSX or windows, see these threads:
- https://github.com/ropensci/git2r/issues/140
......
......@@ -11,7 +11,7 @@ diff_intersect(deData, sample_1, sample_twoes, .intersect_method, ...)
\item{sample_1}{Condition of interest}
\item{.intersect_method}{Which function to use for the intersection? Example \code{\link[coReSCF:s1_gt_s2]{coReSCF::s1_gt_s2()}}}
\item{.intersect_method}{Which function to use for the intersection? Example \code{\link[corescf:s1_gt_s2]{corescf::s1_gt_s2()}}}
\item{...}{Other methods passed to the intersection function}
......@@ -24,7 +24,7 @@ a data.frame
Intersect multiple list of differentially expressed genes.
}
\note{
Assumes the output format from the coreSCF DGE workflow. Table with multiple conditions
Assumes the output format from the corescf DGE workflow. Table with multiple conditions
}
\examples{
\dontrun{
......
......@@ -19,7 +19,7 @@ extractHits(deData, s1, s2, s1Overexpressed = T)
a vector of gene IDs
}
\description{
Extract hits from the table of DGE. Assumes the output format from the coreSCF DGE workflow.
Extract hits from the table of DGE. Assumes the output format from the corescf DGE workflow.
}
\examples{
\dontrun{
......
......@@ -15,7 +15,7 @@ getExpressedGenes(cuff, ...)
A matrix
}
\description{
Wrapper for \code{\link[cummeRbund:repFpkmMatrix]{cummeRbund::repFpkmMatrix()}} and \code{\link[coReSCF:filterByExpression]{coReSCF::filterByExpression()}}
Wrapper for \code{\link[cummeRbund:repFpkmMatrix]{cummeRbund::repFpkmMatrix()}} and \code{\link[corescf:filterByExpression]{corescf::filterByExpression()}}
}
\note{
cummeRbund is now very old and has been superseded by better tools. It should no be the first choice for analysis.
......
......@@ -14,5 +14,5 @@ a data.frame
}
\description{
Removes funky characters from colnames, and converts to lower case, to make them suitable for computational work
Uses \code{\link[coReSCF:pretty_names]{coReSCF::pretty_names()}}
Uses \code{\link[corescf:pretty_names]{corescf::pretty_names()}}
}
......@@ -11,10 +11,10 @@ retainExprGenes(df, id_col = "ensembl_gene_id", ...)
\item{id_col}{the column with gene identifiers. Default ensembl_gene_id}
\item{...}{Arguments to be passed to \code{\link[coReSCF:filterByExpression]{coReSCF::filterByExpression()}}}
\item{...}{Arguments to be passed to \code{\link[corescf:filterByExpression]{corescf::filterByExpression()}}}
}
\description{
#' Deprecated, use \code{\link[coReSCF:filter_expressed_genes]{coReSCF::filter_expressed_genes()}} instead.
#' Deprecated, use \code{\link[corescf:filter_expressed_genes]{corescf::filter_expressed_genes()}} instead.
}
\examples{
\dontrun{
......
......@@ -13,7 +13,7 @@ vec2df(namedVec)
a data.frame
}
\description{
Deprecated, use \code{\link[coReSCF:vec_as_df]{coReSCF::vec_as_df()}} instead.
Deprecated, use \code{\link[corescf:vec_as_df]{corescf::vec_as_df()}} instead.
}
\examples{
\dontrun{
......
library(testthat)
library(coReSCF)
library(corescf)
test_check("coReSCF")
test_check("corescf")
context("CP helper functions")
library("coReSCF")
library("corescf")
## example data
genes1 <- c(
......
context("DF helper functions")
library("coReSCF")
library("corescf")
## mock data
df <- data.frame(
......
......@@ -17,7 +17,7 @@ knitr::opts_chunk$set(
This vignette was created to incorporate some of the use cases left by Holger in `cp_utils.R`.
```{r setup}
library(coReSCF)
library(corescf)
install_package("clusterProfiler")
```
......
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