1. cBioPortalData
  2. R
  3. MultiAssayExperimentData-pkg.R
Browse code

rename package to cBioPortalData

- rename functions:
- downloadcBioPortal -> downloadStudy
- importcBioPortal -> loadStudy

LiNk-NY authored on 04/10/2018 18:57:23
Showing 1 changed files
R/MultiAssayExperimentData-pkg.R
History View file @ fb3cf4b
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deleted file mode 100644
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@@ -1,9 +0,0 @@
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-#' @importFrom S4Vectors isSingleString metadata metadata<- SimpleList DataFrame
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-#' @importFrom SummarizedExperiment SummarizedExperiment
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-#' @importFrom readr read_tsv type_convert
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-#' @importFrom MultiAssayExperiment MultiAssayExperiment ExperimentList
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-#' @importFrom TCGAutils generateMap TCGAbarcode findGRangesCols
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-#' @import RTCGAToolbox
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-#' @importFrom BiocFileCache BiocFileCache bfcquery bfcadd bfcneedsupdate
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-#' bfcdownload bfcrpath bfcremove bfccache
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-NULL
Browse code

import findGRangesCols and use RTCGAToolbox helper

LiNk-NY authored on 20/07/2018 00:03:55
Showing 1 changed files
R/MultiAssayExperimentData-pkg.R
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@@ -2,7 +2,7 @@
2 2 
 #' @importFrom SummarizedExperiment SummarizedExperiment
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 #' @importFrom readr read_tsv type_convert
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 #' @importFrom MultiAssayExperiment MultiAssayExperiment ExperimentList
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-#' @importFrom TCGAutils generateMap TCGAbarcode
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+#' @importFrom TCGAutils generateMap TCGAbarcode findGRangesCols
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 #' @import RTCGAToolbox
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 #' @importFrom BiocFileCache BiocFileCache bfcquery bfcadd bfcneedsupdate
8 8 
 #' bfcdownload bfcrpath bfcremove bfccache
Browse code

import bfccache

LiNk-NY authored on 20/07/2018 00:00:29
Showing 1 changed files
R/MultiAssayExperimentData-pkg.R
History View file @ 9152f4f
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@@ -5,5 +5,5 @@
5 5 
 #' @importFrom TCGAutils generateMap TCGAbarcode
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 #' @import RTCGAToolbox
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 #' @importFrom BiocFileCache BiocFileCache bfcquery bfcadd bfcneedsupdate
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-#' bfcdownload bfcrpath bfcremove
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+#' bfcdownload bfcrpath bfcremove bfccache
9 9 
 NULL
Browse code

add helper for resolving mangled barcodes, resolves #2

LiNk-NY authored on 27/04/2018 19:54:18
Showing 1 changed files
R/MultiAssayExperimentData-pkg.R
History View file @ eae10aa
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@@ -1,7 +1,7 @@
1 1 
 #' @importFrom S4Vectors isSingleString metadata metadata<- SimpleList DataFrame
2 2 
 #' @importFrom SummarizedExperiment SummarizedExperiment
3 3 
 #' @importFrom readr read_tsv type_convert
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-#' @importFrom MultiAssayExperiment MultiAssayExperiment
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+#' @importFrom MultiAssayExperiment MultiAssayExperiment ExperimentList
5 5 
 #' @importFrom TCGAutils generateMap TCGAbarcode
6 6 
 #' @import RTCGAToolbox
7 7 
 #' @importFrom BiocFileCache BiocFileCache bfcquery bfcadd bfcneedsupdate
Browse code

add removeCache function

LiNk-NY authored on 27/03/2018 16:37:55
Showing 1 changed files
R/MultiAssayExperimentData-pkg.R
History View file @ 2ad63e1
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@@ -5,5 +5,5 @@
5 5 
 #' @importFrom TCGAutils generateMap TCGAbarcode
6 6 
 #' @import RTCGAToolbox
7 7 
 #' @importFrom BiocFileCache BiocFileCache bfcquery bfcadd bfcneedsupdate
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-#' bfcdownload bfcrpath
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+#' bfcdownload bfcrpath bfcremove
9 9 
 NULL
Browse code

import BiocFileCache functions

LiNk-NY authored on 27/03/2018 03:53:37
Showing 1 changed files
R/MultiAssayExperimentData-pkg.R
History View file @ 4fcbde9
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@@ -4,4 +4,6 @@
4 4 
 #' @importFrom MultiAssayExperiment MultiAssayExperiment
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 #' @importFrom TCGAutils generateMap TCGAbarcode
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 #' @import RTCGAToolbox
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+#' @importFrom BiocFileCache BiocFileCache bfcquery bfcadd bfcneedsupdate
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+#' bfcdownload bfcrpath
7 9 
 NULL
Browse code

use tsv

LiNk-NY authored on 14/02/2018 17:51:55
Showing 1 changed files
R/MultiAssayExperimentData-pkg.R
History View file @ 7664c95
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@@ -1,6 +1,6 @@
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 #' @importFrom S4Vectors isSingleString metadata metadata<- SimpleList DataFrame
2 2 
 #' @importFrom SummarizedExperiment SummarizedExperiment
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-#' @importFrom readr read_tsv read_delim type_convert
3 
+#' @importFrom readr read_tsv type_convert
4 4 
 #' @importFrom MultiAssayExperiment MultiAssayExperiment
5 5 
 #' @importFrom TCGAutils generateMap TCGAbarcode
6 6 
 #' @import RTCGAToolbox
Browse code

add imports

LiNk-NY authored on 06/02/2018 05:55:25
Showing 1 changed files
R/MultiAssayExperimentData-pkg.R
History View file @ 8dc6956
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@@ -1,4 +1,7 @@
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-#' @importFrom S4Vectors isSingleString metadata SimpleList
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+#' @importFrom S4Vectors isSingleString metadata metadata<- SimpleList DataFrame
2 2 
 #' @importFrom SummarizedExperiment SummarizedExperiment
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-#' @importFrom readr read_tsv
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+#' @importFrom readr read_tsv read_delim type_convert
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+#' @importFrom MultiAssayExperiment MultiAssayExperiment
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+#' @importFrom TCGAutils generateMap TCGAbarcode
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+#' @import RTCGAToolbox
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 NULL
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include additional imports

LiNk-NY authored on 01/02/2018 00:00:42
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R/MultiAssayExperimentData-pkg.R
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@@ -1,3 +1,4 @@
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-#' @importFrom S4Vectors isSingleString metadata
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+#' @importFrom S4Vectors isSingleString metadata SimpleList
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+#' @importFrom SummarizedExperiment SummarizedExperiment
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 #' @importFrom readr read_tsv
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 NULL
Browse code

import additional functions

LiNk-NY authored on 31/01/2018 04:58:06
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R/MultiAssayExperimentData-pkg.R
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@@ -1,2 +1,3 @@
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-#' @importFrom S4Vectors isSingleString
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+#' @importFrom S4Vectors isSingleString metadata
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+#' @importFrom readr read_tsv
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 NULL
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update NAMESPACE

LiNk-NY authored on 11/01/2018 00:24:21
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R/MultiAssayExperimentData-pkg.R
History View file @ 9e52393
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+#' @importFrom S4Vectors isSingleString
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+NULL