@@ -64,6 +64,10 @@ load_biom,

 load_meta,

 load_metaQ,

 load_phenoData,

+loadBiom,

+loadMeta,

+loadMetaQ,

+loadPhenoData,

 makeLabels,

 mergeMRexperiments,

 MRcoefs,

@@ -2,6 +2,7 @@ version 1.15.xx (2016)

 	+ Added 'mergeMRexperiment' function

 	+ Replaced RUnit with testthat library for unit testing

 	+ Adding multiple upgrades and changes throughout

+	+ Deprecated the load_* functions and created load* function.

 version 1.13.xx (2015)

 	+ Upgrade support for biom-format vs. 2.0

 	+ Fixed issue - "MRtable, etc will report NA rows when user requests more features than available"

@@ -9,7 +9,7 @@

 #' @param sl scaling factor for normalized counts.

 #' @param qiimeVersion Format fData according to QIIME specifications (assumes only taxonomy in fData).

 #' @return A biom object.

-#' @seealso \code{\link{load_meta}} \code{\link{load_phenoData}} \code{\link{newMRexperiment}} \code{\link{load_biom}} \code{\link{biom2MRexperiment}}

+#' @seealso \code{\link{loadMeta}} \code{\link{loadPhenoData}} \code{\link{newMRexperiment}} \code{\link{loadBiom}} \code{\link{biom2MRexperiment}}

 MRexperiment2biom <- function(obj,id=NULL,norm=FALSE,log=FALSE,sl=1000,qiimeVersion=TRUE){

     requireNamespace("biomformat")

     id = id

@@ -4,7 +4,7 @@

 #' 

 #' @param obj The biom object file.

 #' @return A MRexperiment object.

-#' @seealso \code{\link{load_meta}} \code{\link{load_phenoData}} \code{\link{newMRexperiment}} \code{\link{load_biom}}

+#' @seealso \code{\link{loadMeta}} \code{\link{loadPhenoData}} \code{\link{newMRexperiment}} \code{\link{loadBiom}}

 #' @examples

 #' 

 #' #library(biomformat)

@@ -13,7 +13,11 @@

 #'  parameters to be passed to the modern version of the function (see table).

 #' @docType package

 #' @export fitMeta

-#' @aliases deprecated_metagenomeSeq_function fitMeta

+#' @aliases deprecated_metagenomeSeq_function fitMeta load_phenoData load_meta load_biom load_metaQ

 #'

 deprecated_metagenomeSeq_function <- function(x, value, ...){return(NULL)}

 fitMeta <- function(...){.Deprecated("fitMeta",package="metagenomeSeq");return(fitLogNormal(...))}

+load_phenoData <- function(...){.Deprecated("load_phenoData",package="metagenomeSeq");return(loadPhenodata(...))}

+load_biom <- function(...){.Deprecated("load_biom",package="metagenomeSeq");return(loadBiom(...))}

+load_meta <- function(...){.Deprecated("load_meta",package="metagenomeSeq");return(loadMeta(...))}

+load_metaQ <- function(...){.Deprecated("load_metaQ",package="metagenomeSeq");return(loadMetaQ(...))}

similarity index 69%

rename from R/load_biom.R

rename to R/loadBiom.R

@@ -4,14 +4,14 @@

 #' 

 #' @param file The biom object filepath.

 #' @return A MRexperiment object.

-#' @seealso \code{\link{load_meta}} \code{\link{load_phenoData}} \code{\link{newMRexperiment}} \code{\link{biom2MRexperiment}}

+#' @seealso \code{\link{loadMeta}} \code{\link{loadPhenoData}} \code{\link{newMRexperiment}} \code{\link{biom2MRexperiment}}

 #' @examples

 #' 

 #' #library(biomformat)

 #' #rich_dense_file = system.file("extdata", "rich_dense_otu_table.biom", package = "biomformat")

-#' #x = load_biom(rich_dense_file)

+#' #x = loadBiom(rich_dense_file)

 #' #x

-load_biom <- function(file){

+loadBiom <- function(file){

 	requireNamespace("biomformat")

 	x = biomformat::read_biom(file);

 	mrobj = biom2MRexperiment(x);

similarity index 79%

rename from R/load_meta.R

rename to R/loadMeta.R

@@ -3,17 +3,17 @@

 #' Load a matrix of OTUs in a tab delimited format

 #' 

 #' 

-#' @aliases load_meta metagenomicLoader

+#' @aliases loadMeta metagenomicLoader

 #' @param file Path and filename of the actual data file.

 #' @param sep File delimiter.

 #' @return A list with objects 'counts' and 'taxa'.

-#' @seealso \code{\link{load_phenoData}}

+#' @seealso \code{\link{loadPhenoData}}

 #' @examples

 #' 

 #' dataDirectory <- system.file("extdata", package="metagenomeSeq")

-#' lung = load_meta(file.path(dataDirectory,"CHK_NAME.otus.count.csv"))

+#' lung = loadMeta(file.path(dataDirectory,"CHK_NAME.otus.count.csv"))

 #' 

-load_meta <- function(file,sep="\t")

+loadMeta <- function(file,sep="\t")

 {

 	dat2 <- read.table(file,header=FALSE,sep=sep,nrows=1,stringsAsFactors=FALSE);

 	subjects <- as.character(dat2[1,-1]);

similarity index 86%

rename from R/load_metaQ.R

rename to R/loadMetaQ.R

@@ -3,15 +3,15 @@

 #' Load a matrix of OTUs in Qiime's format

 #' 

 #' 

-#' @aliases load_metaQ qiimeLoader

+#' @aliases loadMetaQ qiimeLoader

 #' @param file Path and filename of the actual data file.

 #' @return An list with 'counts' containing the count data, 'taxa' containing the otu annotation, and 'otus'.

-#' @seealso \code{\link{load_meta}} \code{\link{load_phenoData}}

+#' @seealso \code{\link{loadMeta}} \code{\link{loadPhenoData}}

 #' @examples

 #' 

 #' # see vignette

 #' 

-load_metaQ <- function(file) {	

+loadMetaQ <- function(file) {	

 	dat2 <- read.delim(file,header=FALSE,stringsAsFactors=FALSE,nrows=1,skip=1);

 	len = ncol(dat2)

 	subjects = as.character(dat2[1,-c(1,len)]);

similarity index 90%

rename from R/load_phenoData.R

rename to R/loadPhenoData.R

@@ -3,18 +3,18 @@

 #' Load a matrix of metadata associated with a study.

 #' 

 #' 

-#' @aliases load_phenoData phenoData

+#' @aliases loadPhenoData phenoData

 #' @param file Path and filename of the actual clinical file.

 #' @param tran Boolean. If the covariates are along the columns and samples

 #' along the rows, then tran should equal TRUE.

 #' @param sep The separator for the file.

 #' @return The metadata as a dataframe.

-#' @seealso \code{\link{load_meta}}

+#' @seealso \code{\link{loadMeta}}

 #' @examples

 #' 

 #' # see vignette

 #' 

-load_phenoData <-function(file,tran=TRUE,sep="\t")

+loadPhenoData <-function(file,tran=TRUE,sep="\t")

 {

 	dat2 <- read.table(file,header=FALSE,sep=sep);

@@ -27,6 +27,6 @@ A biom object.

 Wrapper to convert MRexperiment objects to biom objects.

 }

 \seealso{

-\code{\link{load_meta}} \code{\link{load_phenoData}} \code{\link{newMRexperiment}} \code{\link{load_biom}} \code{\link{biom2MRexperiment}}

+\code{\link{loadMeta}} \code{\link{loadPhenoData}} \code{\link{newMRexperiment}} \code{\link{loadBiom}} \code{\link{biom2MRexperiment}}

 }

@@ -23,6 +23,6 @@ Wrapper to convert biom files to MRexperiment objects.

 #biom2MRexperiment(x)

 }

 \seealso{

-\code{\link{load_meta}} \code{\link{load_phenoData}} \code{\link{newMRexperiment}} \code{\link{load_biom}}

+\code{\link{loadMeta}} \code{\link{loadPhenoData}} \code{\link{newMRexperiment}} \code{\link{loadBiom}}

 }

similarity index 61%

rename from man/load_biom.Rd

rename to man/loadBiom.Rd

@@ -1,10 +1,10 @@

 % Generated by roxygen2: do not edit by hand

-% Please edit documentation in R/load_biom.R

-\name{load_biom}

-\alias{load_biom}

+% Please edit documentation in R/loadBiom.R

+\name{loadBiom}

+\alias{loadBiom}

 \title{Load objects organized in the Biom format.}

 \usage{

-load_biom(file)

+loadBiom(file)

 }

 \arguments{

 \item{file}{The biom object filepath.}

@@ -19,10 +19,10 @@ Wrapper to load Biom formatted object.

 #library(biomformat)

 #rich_dense_file = system.file("extdata", "rich_dense_otu_table.biom", package = "biomformat")

-#x = load_biom(rich_dense_file)

+#x = loadBiom(rich_dense_file)

 #x

 }

 \seealso{

-\code{\link{load_meta}} \code{\link{load_phenoData}} \code{\link{newMRexperiment}} \code{\link{biom2MRexperiment}}

+\code{\link{loadMeta}} \code{\link{loadPhenoData}} \code{\link{newMRexperiment}} \code{\link{biom2MRexperiment}}

 }

similarity index 68%

rename from man/load_meta.Rd

rename to man/loadMeta.Rd

@@ -1,11 +1,11 @@

 % Generated by roxygen2: do not edit by hand

-% Please edit documentation in R/load_meta.R

-\name{load_meta}

-\alias{load_meta}

+% Please edit documentation in R/loadMeta.R

+\name{loadMeta}

+\alias{loadMeta}

 \alias{metagenomicLoader}

 \title{Load a count dataset associated with a study.}

 \usage{

-load_meta(file, sep = "\\t")

+loadMeta(file, sep = "\\t")

 }

 \arguments{

 \item{file}{Path and filename of the actual data file.}

@@ -21,10 +21,10 @@ Load a matrix of OTUs in a tab delimited format

 \examples{

 dataDirectory <- system.file("extdata", package="metagenomeSeq")

-lung = load_meta(file.path(dataDirectory,"CHK_NAME.otus.count.csv"))

+lung = loadMeta(file.path(dataDirectory,"CHK_NAME.otus.count.csv"))

 }

 \seealso{

-\code{\link{load_phenoData}}

+\code{\link{loadPhenoData}}

 }

similarity index 73%

rename from man/load_metaQ.Rd

rename to man/loadMetaQ.Rd

@@ -1,11 +1,11 @@

 % Generated by roxygen2: do not edit by hand

-% Please edit documentation in R/load_metaQ.R

-\name{load_metaQ}

-\alias{load_metaQ}

+% Please edit documentation in R/loadMetaQ.R

+\name{loadMetaQ}

+\alias{loadMetaQ}

 \alias{qiimeLoader}

 \title{Load a count dataset associated with a study set up in a Qiime format.}

 \usage{

-load_metaQ(file)

+loadMetaQ(file)

 }

 \arguments{

 \item{file}{Path and filename of the actual data file.}

@@ -22,6 +22,6 @@ Load a matrix of OTUs in Qiime's format

 }

 \seealso{

-\code{\link{load_meta}} \code{\link{load_phenoData}}

+\code{\link{loadMeta}} \code{\link{loadPhenoData}}

 }

similarity index 75%

rename from man/load_phenoData.Rd

rename to man/loadPhenoData.Rd

@@ -1,11 +1,11 @@

 % Generated by roxygen2: do not edit by hand

-% Please edit documentation in R/load_phenoData.R

-\name{load_phenoData}

-\alias{load_phenoData}

+% Please edit documentation in R/loadPhenoData.R

+\name{loadPhenoData}

+\alias{loadPhenoData}

 \alias{phenoData}

 \title{Load a clinical/phenotypic dataset associated with a study.}

 \usage{

-load_phenoData(file, tran = TRUE, sep = "\\t")

+loadPhenoData(file, tran = TRUE, sep = "\\t")

 }

 \arguments{

 \item{file}{Path and filename of the actual clinical file.}

@@ -27,6 +27,6 @@ Load a matrix of metadata associated with a study.

 }

 \seealso{

-\code{\link{load_meta}}

+\code{\link{loadMeta}}

 }

@@ -4,6 +4,10 @@

 \name{metagenomeSeq-deprecated}

 \alias{deprecated_metagenomeSeq_function}

 \alias{fitMeta}

+\alias{load_biom}

+\alias{load_meta}

+\alias{load_metaQ}

+\alias{load_phenoData}

 \alias{metagenomeSeq-deprecated}

 \alias{metagenomeSeq-deprecated-package}

 \title{Depcrecated functions in the metagenomeSeq package.}

@@ -82,22 +82,22 @@ Data is prepared and formatted as a \texttt{MRexperiment} object. For an overvie

 \subsection{Biom-Format}

-You can load in BIOM file format data, the output of many popular tools out there, using the \texttt{load$\_$biom} function. 

+You can load in BIOM file format data, the output of many popular tools out there, using the \texttt{loadBiom} function. 

 Tthe \texttt{biom2MRexperiment} and \texttt{MRexperiment2biom} functions serve as a gateway between the \texttt{biom-class} object defined in the \textbf{biom} package and a \texttt{MRexperiment-class} object.

 \subsection{Loading count data}

 Following preprocessing and annotation of sequencing data \texttt{metagenomeSeq} requires a count matrix with features along rows and samples along the columns.

 \texttt{metagenomeSeq} includes functions for loading delimited files of counts 

-\texttt{load$\_$meta} and phenodata \texttt{load$\_$phenoData}.

+\texttt{loadMeta} and phenodata \texttt{loadPhenoData}.

 As an example, a portion of the lung microbiome \cite{charlson} 

 OTU matrix is provided in \texttt{metagenomeSeq}'s library "extdata" folder. 

 The OTU matrix is stored as a tab delimited file.

-\texttt{load\_meta} loads the taxa and counts into a list.

+\texttt{loadMeta} loads the taxa and counts into a list.

 <<loadData>>=

 dataDirectory <- system.file("extdata", package="metagenomeSeq")

-lung = load_meta(file.path(dataDirectory,"CHK_NAME.otus.count.csv")) 

+lung = loadMeta(file.path(dataDirectory,"CHK_NAME.otus.count.csv")) 

 dim(lung$counts)

 @

@@ -114,10 +114,10 @@ As our OTUs appear to be in order with the count matrix we loaded earlier, the n

 \textbf{Warning}: features need to have the same names as the rows of the count matrix when we create the MRexperiment object for provenance purposes. 

 \subsection{Loading metadata}

-Phenotype data can be optionally loaded into \texttt{R} with \texttt{load\_phenoData}. This function loads the data as a list.

+Phenotype data can be optionally loaded into \texttt{R} with \texttt{loadPhenoData}. This function loads the data as a list.

 <<loadClin>>=

-clin = load_phenoData(file.path(dataDirectory,"CHK_clinical.csv"),tran=TRUE)

+clin = loadPhenoData(file.path(dataDirectory,"CHK_clinical.csv"),tran=TRUE)

 ord = match(colnames(lung$counts),rownames(clin)) 

 clin = clin[ord,]

 head(clin[1:2,])