Started roxygen2 documentation. Partially added dturtle_sc.

#' Title

#'

#' @param x

#'

#' @return

#' @export

#'

#' @examples

no_na <- function(x){

    return(ifelse(is.na(x), 1, x))

}

#' Filter out

#'

#' @param d

#' @param filter

#'

#' @return

#' @export

#'

#' @examples

smallProportionSD <- function(d, filter) {

    cts <- as.matrix(subset(counts(d), select=-c(gene_id, feature_id)))

    gene.cts <- rowsum(cts, counts(d)$gene_id)

    total.cts <- gene.cts[match(counts(d)$gene_id, rownames(gene.cts)),]

    props <- cts/total.cts

    propSD <- sqrt(matrixStats::rowVars(props))

    return(propSD < filter)

}

#' Title

#'

#' @param tx_mat

#'

#' @return

#' @export

#'

#' @examples

merge_sparse <- function(tx_mat) {

    cnnew <- character()

    rnnew <- character()

    x <- vector()

    i <- numeric()

    j <- numeric()

    for (M in tx_mat) {

        cnold <- colnames(M)

        rnold <- rownames(M)

        cnnew <- union(cnnew,cnold)

        rnnew <- union(rnnew,rnold)

        cindnew <- match(cnold,cnnew)

        rindnew <- match(rnold,rnnew)

        ind <- summary(M)

        i <- c(i,rindnew[ind[,1]])

        j <- c(j,cindnew[ind[,2]])

        x <- c(x,ind[,3])

    }

    return(sparseMatrix(i=i,j=j,x=x,dims=c(length(rnnew),length(cnnew)),dimnames=list(rnnew,cnnew)))

}

#TODO: reevaluate and switch to message

#' Title

#'

#' @param drim

#' @param drim_filt

#'

#' @return

#' @export

#'

#' @examples

count_filtered <- function(drim, drim_filt){

    drim_filt_temp <- dmFilter(drim)

    rm_trans <- nrow(drim@counts)-nrow(drim_filt@counts)

    rm_gene <- length(drim@counts@partitioning)-length(drim_filt@counts@partitioning)

    print(paste0("Removed ", rm_trans," (",formatC(((rm_trans)/nrow(drim@counts))*100, 2, format = "f"),"%) of ",nrow(drim@counts)," transcripts due to filters."))

    print(paste0("Removed ", rm_gene," (",formatC(((rm_gene)/length(drim@counts@partitioning))*100, 2, format = "f"),"%) of ",length(drim@counts@partitioning)," genes due to filters."))

    print(paste0("Of the removed transcripts: ", nrow(drim@counts)-nrow(drim_filt_temp@counts)," (",formatC(((nrow(drim@counts)-nrow(drim_filt_temp@counts))/rm_trans)*100, 2, format = "f"),"%) had no expression."))

    print(paste0("This explains ", length(drim@counts@partitioning)-length(drim_filt_temp@counts@partitioning)," (",formatC(((length(drim@counts@partitioning)-length(drim_filt_temp@counts@partitioning))/rm_gene)*100, 2, format = "f"),"%) of the removed genes."))

    print(paste0("--> Proceed with ",length(drim_filt@counts@partitioning)," genes and ",nrow(drim_filt@counts)," transcripts."))

}

#' Title

#'

#' @param gID

#' @param dtu

#'

#' @return

#' @export

#'

#' @examples

get_diff <- function(gID, dtu){

    group <- dtu$group

    y <- data.frame(row.names = rownames(dtu$drim@fit_full[[gID]]))

    y$a <- apply(dtu$drim@fit_full[[gID]][, which(group==levels(group)[1])], 1, unique)

    y$b <- apply(dtu$drim@fit_full[[gID]][, which(group==levels(group)[2])], 1, unique)

    y$diff <- y$a-y$b

    return(y)

}

#' Title

#'

#' @param dtu_table

#' @param dtu

#'

#' @return

#' @export

#'

#' @examples

add_max_delta <- function(dtu_table, dtu){

    getmax <- function(gID){

        y <- get_diff(gID, dtu)

        #get absoulte maximum while preserving sign

        return(y$diff[which.max(abs(y$diff))])

    }

    dtu_table[[paste0("max(",levels(dtu$group)[1], "-",levels(dtu$group)[2],")")]] <- as.numeric(sapply(dtu_table$geneID, FUN = getmax))

    return(dtu_table)

}

% Generated by roxygen2: do not edit by hand

% Please edit documentation in R/helper_functions.R

\name{add_max_delta}

\alias{add_max_delta}

\title{Title}

\usage{

add_max_delta(dtu_table, dtu)

}

\arguments{

\item{dtu}{}

}

\value{

}

\description{

Title

}

% Generated by roxygen2: do not edit by hand

% Please edit documentation in R/dtu_analysis.R

\name{add_to_seurat}

\alias{add_to_seurat}

\title{Title}

\usage{

add_to_seurat(tx_mat, seurat_obj)

}

\arguments{

\item{seurat_obj}{}

}

\value{

}

\description{

Title

}

% Generated by roxygen2: do not edit by hand

% Please edit documentation in R/helper_functions.R

\name{count_filtered}

\alias{count_filtered}

\title{Title}

\usage{

count_filtered(drim, drim_filt)

}

\arguments{

\item{drim_filt}{}

}

\value{

}

\description{

Title

}

% Generated by roxygen2: do not edit by hand

% Please edit documentation in R/visualization.R

\name{create_dtu_table}

\alias{create_dtu_table}

\title{Title}

\usage{

create_dtu_table(

  dtu,

  gene_name_info = NULL,

  gene_chromosome_info = NULL,

  gene_description = NULL

)

}

\arguments{

\item{gene_description}{}

}

\value{

}

\description{

Title

}