@@ -54,6 +54,7 @@ Collate:

     'deconrnaseqParam-class.R'

     'epicParam-class.R'

     'lute_cell-scale-factors.R'

+    'lute_cellScaleFactors.R'

     'lute_experiment.R'

     'lute_framework.R'

     'lute_metadata.R'

@@ -10,12 +10,11 @@ export(deconvolution.results.plots)

 export(deconvolution.results.plots.permutations)

 export(deconvolution.results.table)

 export(epicParam)

-export(get_filter_group_markers)

+export(get_csf_reference)

 export(independentbulkParam)

 export(lute)

 export(lute_supported_deconvolution_algorithms)

 export(make_lpv)

-export(marker_overlaps)

 export(markers_by_group)

 export(meanratiosParam)

 export(music2Param)

@@ -8,7 +8,7 @@

 # this is the main task for parallel selection of group markers

 .get.group.markers.iter <- function(task.iter, sce, assay.name, 

                                    celltype.variable, markers.per.type,

-                                   downsample.within.group){

+                                   downsample.within.group, verbose = F){

   if(verbose){message("Getting markers for group id: ", task.iter, "...")}

   filter <- sce[[group.variable]] == task.iter; sce.filter <- sce[,filter]

new file mode 100644

@@ -0,0 +1,35 @@

+% Generated by roxygen2: do not edit by hand

+% Please edit documentation in R/lute_cellScaleFactors.R

+\name{get_csf_reference}

+\alias{get_csf_reference}

+\title{get_csf_reference}

+\usage{

+get_csf_reference(user.celltypes.vector = NULL, prefer.orthogonal = TRUE)

+}

+\arguments{

+\item{user.celltypes.vector}{Vector of user-specified cell types.}

+

+\item{prefer.orthogonal}{Whether to prefer expression-orthogonal values (if 

+TRUE, removes expression-based values).}

+}

+\value{

+Table of type "data.frame" or "tibble".

+}

+\description{

+Retrieves the cell scale factors (csf) reference from the cellScaleFactors package.

+}

+\details{

+Returns a table of cell scale factors from various data sources. The 

+cell scale factors reference table has the following columns:

+

+1. cell_type : Label of the cell type for the scale factor (e.g. neuron, T cell, etc.)

+2. tissue : Label of the tissue of origin (e.g. brain, blood, etc.)

+3. scale.factor.value : Point scale factor value prior to additional normalization

+4. scale.factor.type : Label for scale factor type (e.g. cell or nuclear area, etc.)

+5. scale.factor.data.source : Label for scale factor source (e.g. osmFISH, 

+housekeeping gene expression, etc.)

+6. citation.s : Citations of source studies from which original measures or 

+measure summaries were made.

+

+Details about the reference table can be found in the cellScaleFactors package.

+}

deleted file mode 100644

@@ -1,50 +0,0 @@

-% Generated by roxygen2: do not edit by hand

-% Please edit documentation in R/lute_typemarker-selection.R

-\name{get_filter_group_markers}

-\alias{get_filter_group_markers}

-\title{get_filter_group_markers}

-\usage{

-get_filter_group_markers(

-  group.markers,

-  minimum.group.overlap.rate = 0.5,

-  verbose = TRUE

-)

-}

-\arguments{

-\item{minimum.group.overlap.rate}{Minimum amount of overlap by group. Should be a 

-fraction of the total groups in the data (e.g. 0.2 means the marker is 

-overlapping in 20% of groups).}

-

-\item{verbose}{Whether to show verbose status messages.}

-

-\item{markers.list}{List of gene markers, organized by groups studied (e.g. 

-returned from calling \code{marker_overlaps()} (see \code{?marker_overlaps} 

-for details).}

-}

-\value{

-List containing markers for removal/filtering, with metadata about the

-different filter parameters and type marker selection results.

-}

-\description{

-Get concordant, overlapping markers from a list of markers by group.

-}

-\details{

-Performs the following marker filter steps:

-* Uniqueness: Removes duplicate markers across type lists.

-* Concordance: Removes markers which aren't specific to the same type across 

-groups.

-* Overlap: Removes markers below an overlap rate, defined using the 

-\code{min.group.overlap.rate} argument.

-}

-\examples{

-set.seed(0)

-sce.example <- random_sce(num.cells = 100, num.genes = 1000)

-sce.example[["sample_id"]] <- c(rep("sample1", 50), rep("sample2", 50))

-group.markers <- markers_by_group(sce.example, markers.per.type = 5)

-markers.filter.vector <- get_filter_group_markers(group.markers)

-length(markers.filter.vector)

-

-}

-\seealso{

-\code{markers_by_group}, \code{marker_overlaps}

-}

deleted file mode 100644

@@ -1,28 +0,0 @@

-% Generated by roxygen2: do not edit by hand

-% Please edit documentation in R/lute_typemarker-selection.R

-\name{marker_overlaps}

-\alias{marker_overlaps}

-\title{marker_overlaps}

-\usage{

-marker_overlaps(group.markers, marker.filter.vector = NULL)

-}

-\arguments{

-\item{group.markers}{Group-specific markers list returned from 

-\code{markers_by_group} (see \code{?markers_by_group} for details).}

-

-\item{marker.filter.vector}{Vector of markers to compare (exclude all 

-additional markers).}

-}

-\value{

-Table containing marker overlap info.

-}

-\description{

-Gets marker overlap info among groups.

-}

-\examples{

-sce.example <- random_sce(num.cells = 100, num.genes = 100)

-sce.example[["sample_id"]] <- c(rep("sample1", 20), rep("sample2", 80))

-group.markers <- markers_by_group(sce.example)

-group.overlaps <- marker_overlaps(group.markers)

-

-}

@@ -9,9 +9,11 @@ markers_by_group(

   group.variable = "sample_id",

   celltype.variable = "celltype",

   assay.name = "counts",

-  markers.per.type = 20,

+  markers.per.type = 100,

   typemarker.algorithm = "meanratios",

   return.type = "list",

+  downsample.within.group = T,

+  parallelize = T,

   verbose = FALSE

 )

 }

@@ -34,6 +36,12 @@ for marker selection.}

 \item{return.type}{Format of return data, either "list" or "table".}

+\item{downsample.within.group}{Whether to downsample on cell types prior to 

+marker selection (performed *within* groups)}

+

+\item{parallelize}{Whether to use parallelization (mclapply) when getting 

+markers by group. Otherwise uses lapply.}

+

 \item{verbose}{Whether to show verbose status messages.}

 }

 \value{

@@ -44,14 +52,15 @@ organized by group IDs.

 Get gene markers organized by groups.

 }

 \details{

-Gets the group markers for all individual specified groups, where

-"group" here means donor, batch, or some other set of cells over which we

-may be concerned about marker consistency.

+Gets the within-group cell type markers.

 }

 \examples{

 sce.example <- random_sce(num.cells = 100, num.genes = 100)

 sce.example[["sample_id"]] <- c(rep("sample1", 10), rep("sample2", 80), rep("sample1", 10))

 group.markers <- markers_by_group(sce.example)

+

+

+

 }

 \seealso{

 \code{filter_group_markers}