1. TENxIO
  2. man
  3. TENxFragments.Rd
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rename roi to which

LiNk-NY authored on 05/10/2022 22:16:03
Showing 1 changed files
man/TENxFragments.Rd
History View file @ 334a064
... ... 
@@ -4,7 +4,7 @@
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 \alias{TENxFragments}
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 \title{TENxFragments: Import fragments files from 10X}
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 \usage{
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-TENxFragments(resource, yieldSize = 200, roi = GRanges(), ...)
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+TENxFragments(resource, yieldSize = 200, which = GRanges(), ...)
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 }
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 \arguments{
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 \item{resource}{character(1) The file path to the fragments resource, usually
... ... 
@@ -13,7 +13,7 @@ a compressed tabix file with extension \code{.tsv.gz}.}
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 \item{yieldSize}{numeric() The number of records to read by default, 200
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 records will be imported. A warning will be emitted if not modified.}
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-\item{roi}{GRanges() A GRanges indicating the regions of interest. This
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+\item{which}{GRanges() A GRanges indicating the regions of interest. This
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 get sent to \code{RSamtools} as the \code{param} input.}
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 \item{...}{Further arguments to the class generator function (currently not
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add and update \value sections in docs

LiNk-NY authored on 24/08/2022 22:58:22
Showing 1 changed files
man/TENxFragments.Rd
History View file @ fd5d3c1
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@@ -19,6 +19,9 @@ get sent to \code{RSamtools} as the \code{param} input.}
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 \item{...}{Further arguments to the class generator function (currently not
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 used)}
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 }
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+\value{
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+A \code{RaggedExperiment} object class
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+}
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 \description{
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 TENxFragments: Import fragments files from 10X
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 }
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add fragments file and index example for TENxFragments

LiNk-NY authored on 03/08/2022 16:36:44
Showing 1 changed files
man/TENxFragments.Rd
History View file @ 77c98de
... ... 
@@ -24,12 +24,13 @@ TENxFragments: Import fragments files from 10X
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 }
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 \examples{
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-con <- TENxFile("~/data/10x/pbmc_3k/pbmc_granulocyte_sorted_3k_filtered_feature_bc_matrix.h5")
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-con
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-sce <- import(con)
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+fr <- system.file(
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+    "extdata", "pbmc_3k_atac_ex_fragments.tsv.gz",
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+    package = "TENxIO", mustWork = TRUE
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+)
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-fr <- "~/data/10x/pbmc_3k/pbmc_granulocyte_sorted_3k_atac_fragments.tsv.gz"
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 tfr <- TENxFragments(fr)
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+
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 fra <- import(tfr)
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 }
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documentation updates

LiNk-NY authored on 14/07/2022 16:58:36
Showing 1 changed files
man/TENxFragments.Rd
History View file @ bc9ed23
... ... 
@@ -2,8 +2,7 @@
2 2 
 % Please edit documentation in R/TENxFragments-class.R
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 \name{TENxFragments}
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 \alias{TENxFragments}
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-\alias{TENxFragments-class}
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-\title{Import fragments files from 10X}
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+\title{TENxFragments: Import fragments files from 10X}
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 \usage{
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 TENxFragments(resource, yieldSize = 200, roi = GRanges(), ...)
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 }
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@@ -12,7 +11,7 @@ TENxFragments(resource, yieldSize = 200, roi = GRanges(), ...)
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 a compressed tabix file with extension \code{.tsv.gz}.}
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 \item{yieldSize}{numeric() The number of records to read by default, 200
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-records will be imported. A warning will be emmitted if not modified.}
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+records will be imported. A warning will be emitted if not modified.}
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 \item{roi}{GRanges() A GRanges indicating the regions of interest. This
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 get sent to \code{RSamtools} as the \code{param} input.}
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@@ -21,7 +20,7 @@ get sent to \code{RSamtools} as the \code{param} input.}
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 used)}
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 }
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 \description{
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-Import fragments files from 10X
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+TENxFragments: Import fragments files from 10X
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 }
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 \examples{
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set yieldSize to default when roi present

LiNk-NY authored on 16/06/2022 18:04:58
Showing 1 changed files
man/TENxFragments.Rd
History View file @ a3ac962
... ... 
@@ -26,6 +26,7 @@ Import fragments files from 10X
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 \examples{
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 con <- TENxFile("~/data/10x/pbmc_3k/pbmc_granulocyte_sorted_3k_filtered_feature_bc_matrix.h5")
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+con
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 sce <- import(con)
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 fr <- "~/data/10x/pbmc_3k/pbmc_granulocyte_sorted_3k_atac_fragments.tsv.gz"
Browse code

move TENxFragments class

LiNk-NY authored on 03/06/2022 19:53:40
Showing 1 changed files
man/TENxFragments.Rd
History View file @ 0bb9257
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new file mode 100644
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@@ -0,0 +1,35 @@
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+% Generated by roxygen2: do not edit by hand
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+% Please edit documentation in R/TENxFragments-class.R
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+\name{TENxFragments}
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+\alias{TENxFragments}
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+\alias{TENxFragments-class}
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+\title{Import fragments files from 10X}
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+\usage{
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+TENxFragments(resource, yieldSize = 200, roi = GRanges(), ...)
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+}
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+\arguments{
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+\item{resource}{character(1) The file path to the fragments resource, usually
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+a compressed tabix file with extension \code{.tsv.gz}.}
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+
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+\item{yieldSize}{numeric() The number of records to read by default, 200
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+records will be imported. A warning will be emmitted if not modified.}
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+
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+\item{roi}{GRanges() A GRanges indicating the regions of interest. This
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+get sent to \code{RSamtools} as the \code{param} input.}
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+
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+\item{...}{Further arguments to the class generator function (currently not
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+used)}
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+}
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+\description{
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+Import fragments files from 10X
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+}
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+\examples{
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+
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+con <- TENxFile("~/data/10x/pbmc_3k/pbmc_granulocyte_sorted_3k_filtered_feature_bc_matrix.h5")
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+sce <- import(con)
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+
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+fr <- "~/data/10x/pbmc_3k/pbmc_granulocyte_sorted_3k_atac_fragments.tsv.gz"
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+tfr <- TENxFragments(fr)
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+fra <- import(tfr)
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+
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+}