1. scAnnotatR
  2. man
  3. parent.Rd
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merge separate methods for Seurat and SCE signatures into one function

nttvy authored on 29/07/2021 22:23:02
Showing 1 changed files
man/parent.Rd
History View file @ a212ecf
... ... 
@@ -19,8 +19,9 @@ Returns the parent of the cell type corresponding to the given classifier.
19 19 
 data("tirosh_mel80_example")
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 selected_marker_genes_B = c("CD19", "MS4A1", "CD79A")
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 set.seed(123)
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-classifier_b <- train_classifier(train_obj = tirosh_mel80_example,
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-marker_genes = selected_marker_genes_B, cell_type = "B cells")
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+classifier_b <- train_classifier(train_obj = tirosh_mel80_example,
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+assay = 'RNA', slot = 'counts', marker_genes = selected_marker_genes_B,
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+cell_type = "B cells", tag_slot = 'active.ident')
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 parent(classifier_b)
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 }
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replace core clf by caret_model replace all other clf by classifiers

Former-commit-id: 91ec8da24f45c110ab4f2e728ab71e9c1d255ca8

nttvy authored on 22/07/2021 13:51:48
Showing 1 changed files
man/parent.Rd
History View file @ adb6f19
... ... 
@@ -19,8 +19,8 @@ Returns the parent of the cell type corresponding to the given classifier.
19 19 
 data("tirosh_mel80_example")
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 selected_marker_genes_B = c("CD19", "MS4A1", "CD79A")
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 set.seed(123)
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-clf_b <- train_classifier(train_obj = tirosh_mel80_example,
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+classifier_b <- train_classifier(train_obj = tirosh_mel80_example,
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 marker_genes = selected_marker_genes_B, cell_type = "B cells")
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-parent(clf_b)
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+parent(classifier_b)
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 }
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change features to marker_genes

Former-commit-id: b8f82581ead9bfe31c088db02857a1d1c996d832

nttvy authored on 22/07/2021 11:32:05
Showing 1 changed files
man/parent.Rd
History View file @ 7e9ee09
... ... 
@@ -17,10 +17,10 @@ Returns the parent of the cell type corresponding to the given classifier.
17 17 
 }
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 \examples{
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 data("tirosh_mel80_example")
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-selected_features_B = c("CD19", "MS4A1", "CD79A")
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+selected_marker_genes_B = c("CD19", "MS4A1", "CD79A")
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 set.seed(123)
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 clf_b <- train_classifier(train_obj = tirosh_mel80_example,
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-features = selected_features_B, cell_type = "B cells")
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+marker_genes = selected_marker_genes_B, cell_type = "B cells")
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 parent(clf_b)
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 }
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rename package from scClassifR to scAnnotatR

Former-commit-id: 9823f9b8cf0ad38ebbe2bcd6f870a63a98c29d07

nttvy authored on 01/07/2021 12:02:51
Showing 1 changed files
man/parent.Rd
History View file @ 499496a
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@@ -7,7 +7,7 @@
7 7 
 parent(classifier)
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 }
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 \arguments{
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-\item{classifier}{scClassifR object}
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+\item{classifier}{scAnnotatR object}
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 }
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 \value{
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 Parent model of object
Browse code

rename package

Former-commit-id: c41bda4739a20cb0a346da77aaa02256d756b67f

nttvy authored on 29/12/2020 00:49:20
Showing 1 changed files
man/parent.Rd
History View file @ 0ed9c39
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@@ -7,7 +7,7 @@
7 7 
 parent(classifier)
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 }
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 \arguments{
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-\item{classifier}{scTypeR object}
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+\item{classifier}{scClassifR object}
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 }
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 \value{
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 Parent model of object
Browse code

convert single-method generics to plain-old functions

Former-commit-id: e52b32b4499d2b03f0175aea229f12e4ceb43999

nttvy authored on 24/12/2020 16:11:58
Showing 1 changed files
man/parent.Rd
History View file @ 6c81450
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@@ -2,12 +2,9 @@
2 2 
 % Please edit documentation in R/class.R
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 \name{parent}
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 \alias{parent}
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-\alias{parent,scTypeR-method}
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 \title{parent}
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 \usage{
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 parent(classifier)
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-
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-\S4method{parent}{scTypeR}(classifier)
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 }
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 \arguments{
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 \item{classifier}{scTypeR object}
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group non exported functions

Former-commit-id: 6c0f23354428e151ce50a784d61b6a9bcad0861a

nttvy authored on 22/12/2020 16:30:32
Showing 1 changed files
man/parent.Rd
History View file @ 34c7392
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@@ -2,9 +2,12 @@
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 % Please edit documentation in R/class.R
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 \name{parent}
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 \alias{parent}
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+\alias{parent,scTypeR-method}
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 \title{parent}
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 \usage{
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 parent(classifier)
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+
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+\S4method{parent}{scTypeR}(classifier)
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 }
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 \arguments{
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 \item{classifier}{scTypeR object}
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Change package name

Former-commit-id: af53b823be827fde1d0a8435136b9455293ccbdc

nttvy authored on 01/12/2020 09:03:46
Showing 1 changed files
man/parent.Rd
History View file @ 5796ba1
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@@ -7,7 +7,7 @@
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 parent(classifier)
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 }
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 \arguments{
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-\item{classifier}{SingleCellClassR object}
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+\item{classifier}{scTypeR object}
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 }
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 \value{
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 Parent model of object
Browse code

Initial commit

Former-commit-id: c30d5e0eb17749597b12316855f05517b93b7be9

Johannes Griss authored on 10/11/2020 10:34:39
Showing 1 changed files
man/parent.Rd
History View file @ 0065b78
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new file mode 100644
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@@ -0,0 +1,26 @@
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+% Generated by roxygen2: do not edit by hand
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+% Please edit documentation in R/class.R
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+\name{parent}
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+\alias{parent}
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+\title{parent}
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+\usage{
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+parent(classifier)
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+}
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+\arguments{
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+\item{classifier}{SingleCellClassR object}
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+}
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+\value{
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+Parent model of object
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+}
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+\description{
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+Returns the parent of the cell type corresponding to the given classifier.
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+}
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+\examples{
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+data("tirosh_mel80_example")
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+selected_features_B = c("CD19", "MS4A1", "CD79A")
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+set.seed(123)
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+clf_b <- train_classifier(train_obj = tirosh_mel80_example,
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+features = selected_features_B, cell_type = "B cells")
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+parent(clf_b)
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+
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+}