Bioconductor Code: Browse

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Commit 09102021

Bhattacharya authored on 10/09/2021 17:26:18
Showing 19 changed files

.Rhistory index 83cc101..0000000
.Rproj.user/3F8D143E/build_options index 4089afd..0000000
.Rproj.user/3F8D143E/cpp-definition-cache index 0637a08..0000000
.Rproj.user/3F8D143E/pcs/debug-breakpoints.pper index 4893a8a..0000000
.Rproj.user/3F8D143E/pcs/files-pane.pper index bf73e8f..0000000
.Rproj.user/3F8D143E/pcs/source-pane.pper index a528f3b..0000000
.Rproj.user/3F8D143E/pcs/windowlayoutstate.pper index 86077ea..0000000
.Rproj.user/3F8D143E/pcs/workbench-pane.pper index c38a0b3..0000000
.Rproj.user/3F8D143E/persistent-state index 7b6ff7a..0000000
.Rproj.user/3F8D143E/rmd-outputs index 3f2ff2d..0000000
.Rproj.user/3F8D143E/saved_source_markers index 2b1bef1..0000000
.Rproj.user/3F8D143E/sources/prop/47696581 index bb27690..0000000
.Rproj.user/3F8D143E/sources/prop/INDEX index a933385..0000000
.Rproj.user/3F8D143E/sources/s-5E981E40/lock_file index e69de29..0000000
.Rproj.user/3F8D143E/vcs_options index 2bfb049..0000000
.Rproj.user/shared/notebooks/patch-chunk-names index e69de29..0000000
.Rproj.user/shared/notebooks/paths index efade95..0000000
R/OverlappingGenes.r index 1fd4a5a..f241bd8 100644
man/hello.Rd index 0fa7c4b..0000000

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                     -library(roxygen2)
                     -roxygenize()
                     -roxygenize()
                     -warnings()
                     -roxygenize()
                     -roxygenize()
                     -library(nanotatoR)

.Rproj.user/3F8D143E/build_options

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                     -auto_roxygenize_for_build_and_reload="0"
                     -auto_roxygenize_for_build_package="1"
                     -auto_roxygenize_for_check="1"
                     -live_preview_website="0"
                     -makefile_args=""
                     -preview_website="1"
                     -website_output_format="all"

.Rproj.user/3F8D143E/cpp-definition-cache

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                     -[]
                     \ No newline at end of file

.Rproj.user/3F8D143E/pcs/debug-breakpoints.pper

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                     -{
                     -    "debugBreakpointsState": {
                     -        "breakpoints": []
                     -    }
                     -}
                     \ No newline at end of file

.Rproj.user/3F8D143E/pcs/files-pane.pper

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@@ -1,9 +0,0 @@
                     -{
                     -    "sortOrder": [
                     -        {
                     -            "columnIndex": 2,
                     -            "ascending": true
                     -        }
                     -    ],
                     -    "path": "C:/Suro/nanotatoR/nanotatoR"
                     -}
                     \ No newline at end of file

.Rproj.user/3F8D143E/pcs/source-pane.pper

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                     -{
                     -    "activeTab": -1
                     -}
                     \ No newline at end of file

.Rproj.user/3F8D143E/pcs/windowlayoutstate.pper

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@@ -1,14 +0,0 @@
                     -{
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                     -        "windowheight": 996
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                     -}
                     \ No newline at end of file

.Rproj.user/3F8D143E/pcs/workbench-pane.pper

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                     -{
                     -    "TabSet1": 4,
                     -    "TabSet2": 0,
                     -    "TabZoom": {}
                     -}
                     \ No newline at end of file

.Rproj.user/3F8D143E/persistent-state

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@@ -1,8 +0,0 @@
                     -build-last-errors="[]"
                     -build-last-errors-base-dir="C:/Suro/nanotatoR/nanotatoR/"
                     -build-last-outputs="[{\"type\":0,\"output\":\"==> Rcmd.exe INSTALL --preclean --no-multiarch --with-keep.source nanotatoR\\n\\n\"},{\"type\":1,\"output\":\"* installing to library 'C:/Users/sbhattach2/OneDrive - Children's National Hospital/Documents/R/win-library/4.1'\\r\\n\"},{\"type\":1,\"output\":\"\"},{\"type\":1,\"output\":\"* installing *source* package 'nanotatoR' ...\\r\\n\"},{\"type\":1,\"output\":\"\"},{\"type\":1,\"output\":\"** using staged installation\\r\\n\"},{\"type\":1,\"output\":\"\"},{\"type\":1,\"output\":\"** R\\r\\n\"},{\"type\":1,\"output\":\"\"},{\"type\":1,\"output\":\"** inst\\r\\n\"},{\"type\":1,\"output\":\"\"},{\"type\":1,\"output\":\"** byte-compile and prepare package for lazy loading\\r\\n\"},{\"type\":1,\"output\":\"\"},{\"type\":1,\"output\":\"** help\\r\\n\"},{\"type\":1,\"output\":\"\"},{\"type\":1,\"output\":\"*** installing help indices\\r\\n\"},{\"type\":1,\"output\":\"\"},{\"type\":1,\"output\":\"  converting help for package 'nanotatoR'\\r\\n\"},{\"type\":1,\"output\":\"\"},{\"type\":1,\"output\":\"    finding HTML links ...\"},{\"type\":1,\"output\":\" done\\r\\n\"},{\"type\":1,\"output\":\"\"},{\"type\":1,\"output\":\"    BNDBfrequency                           html  \\r\\n\"},{\"type\":1,\"output\":\"    DGVfrequency                            html  \"},{\"type\":1,\"output\":\"\\r\\n\"},{\"type\":1,\"output\":\"    Decipherfrequency                       html  \"},{\"type\":1,\"output\":\"\\r\\n\"},{\"type\":1,\"output\":\"    FamilyInfoPrep                          html  \\r\\n\"},{\"type\":1,\"output\":\"    OverlapRNAseq                           html  \"},{\"type\":1,\"output\":\"\\r\\n\"},{\"type\":1,\"output\":\"    OverlapRNAseq_solo                      html  \\r\\n\"},{\"type\":1,\"output\":\"    RNAseqcombine                           html  \\r\\n\"},{\"type\":1,\"output\":\"    RNAseqcombine_solo                      html  \"},{\"type\":1,\"output\":\"\\r\\n\"},{\"type\":1,\"output\":\"    SVexpression_duo_trio                   html  \"},{\"type\":1,\"output\":\"\\r\\n\"},{\"type\":1,\"output\":\"    SVexpression_solo                       html  \\r\\n\"},{\"type\":1,\"output\":\"    buildrunBNBedFiles                      html  \"},{\"type\":1,\"output\":\"\\r\\n\"},{\"type\":1,\"output\":\"    clinvar_gene                            html  \\r\\n\"},{\"type\":1,\"output\":\"    extract_clinvar_mod                     html  \"},{\"type\":1,\"output\":\"\\r\\n\"},{\"type\":1,\"output\":\"    gene_extraction                         html  \\r\\n\"},{\"type\":1,\"output\":\"    gene_list_generation                    html  \"},{\"type\":1,\"output\":\"\\r\\n\"},{\"type\":1,\"output\":\"    gtr_gene                                html  \\r\\n\"},{\"type\":1,\"output\":\"    hello                                   html  \"},{\"type\":1,\"output\":\"\\r\\n\"},{\"type\":1,\"output\":\"    internalFrequencyTrio_Duo               html  \"},{\"type\":1,\"output\":\"\\r\\n\"},{\"type\":1,\"output\":\"    internalFrequency_solo                  html  \"},{\"type\":1,\"output\":\"\\r\\n\"},{\"type\":1,\"output\":\"    makeInternalBNDatabase                  html  \"},{\"type\":1,\"output\":\"\\r\\n\"},{\"type\":1,\"output\":\"    mergingSMAP_SE                          html  \"},{\"type\":1,\"output\":\"\\r\\n\"},{\"type\":1,\"output\":\"    mergingSMAP_SVMerge                     html  \\r\\n\"},{\"type\":1,\"output\":\"    merging_SE_SVMerge                      html  \"},{\"type\":1,\"output\":\"\\r\\n\"},{\"type\":1,\"output\":\"    nanotatoR                               html  \"},{\"type\":1,\"output\":\"\\r\\n\"},{\"type\":1,\"output\":\"    nanotatoR_Duo_SVmerge                   html  \"},{\"type\":1,\"output\":\"\\r\\n\"},{\"type\":1,\"output\":\"    nanotatoR_SVmerge_Trio                  html  \"},{\"type\":1,\"output\":\"\\r\\n\"},{\"type\":1,\"output\":\"    nanotatoR_main_Duo_SE                   html  \"},{\"type\":1,\"output\":\"\\r\\n\"},{\"type\":1,\"output\":\"    nanotatoR_main_Solo_SE                  html  \"},{\"type\":1,\"output\":\"\\r\\n\"},{\"type\":1,\"output\":\"    nanotatoR_main_Solo_SVmerge             html  \"},{\"type\":1,\"output\":\"\\r\\n\"},{\"type\":1,\"output\":\"    nanotatoR_main_Trio_SE                  html  \"},{\"type\":1,\"output\":\"\\r\\n\"},{\"type\":1,\"output\":\"    nonOverlapGenes                         html  \"},{\"type\":1,\"output\":\"\\r\\n\"},{\"type\":1,\"output\":\"    nonOverlapRNAseq                        html  \"},{\"type\":1,\"output\":\"\\r\\n\"},{\"type\":1,\"output\":\"    nonOverlapRNAseq_solo                   html  \"},{\"type\":1,\"output\":\"\\r\\n\"},{\"type\":1,\"output\":\"    nonOverlappingDNGenes                   html  \"},{\"type\":1,\"output\":\"\\r\\n\"},{\"type\":1,\"output\":\"    nonOverlappingUPGenes                   html  \"},{\"type\":1,\"output\":\"\\r\\n\"},{\"type\":1,\"output\":\"    omim_gene                               html  \"},{\"type\":1,\"output\":\"\\r\\n\"},{\"type\":1,\"output\":\"    overlapGenes                            html  \"},{\"type\":1,\"output\":\"\\r\\n\"},{\"type\":1,\"output\":\"    overlapnearestgeneSearch                html  \"},{\"type\":1,\"output\":\"\\r\\n\"},{\"type\":1,\"output\":\"    overlappingGenes                        html  \\r\\n\"},{\"type\":1,\"output\":\"    phenoextractHPO_mod                     html  \"},{\"type\":1,\"output\":\"\\r\\n\"},{\"type\":1,\"output\":\"    readBNBedFiles                          html  \\r\\n\"},{\"type\":1,\"output\":\"    readSMap                                html  \"},{\"type\":1,\"output\":\"\\r\\n\"},{\"type\":1,\"output\":\"    readSMap_DLE                            html  \\r\\n\"},{\"type\":1,\"output\":\"    reading_GTR                             html  \"},{\"type\":1,\"output\":\"\\r\\n\"},{\"type\":1,\"output\":\"    reading_mim2gene                        html  \\r\\n\"},{\"type\":1,\"output\":\"    run_bionano_filter_SE_Trio              html  \"},{\"type\":1,\"output\":\"\\r\\n\"},{\"type\":1,\"output\":\"    run_bionano_filter_SE_duo               html  \"},{\"type\":1,\"output\":\"\\r\\n\"},{\"type\":1,\"output\":\"    run_bionano_filter_SE_solo              html  \"},{\"type\":1,\"output\":\"\\r\\n\"},{\"type\":1,\"output\":\"    run_bionano_filter_SVMerge_Trio         html  \"},{\"type\":1,\"output\":\"\\r\\n\"},{\"type\":1,\"output\":\"    run_bionano_filter_SVMerge_duo          html  \\r\\n\"},{\"type\":1,\"output\":\"    run_bionano_filter_SVMerge_solo         html  \"},{\"type\":1,\"output\":\"\\r\\n\"},{\"type\":1,\"output\":\"\"},{\"type\":1,\"output\":\"** building package indices\\r\\n\"},{\"type\":1,\"output\":\"\"},{\"type\":1,\"output\":\"** installing vignettes\\r\\n\"},{\"type\":1,\"output\":\"\"},{\"type\":1,\"output\":\"** testing if installed package can be loaded from temporary location\\r\\n\"},{\"type\":1,\"output\":\"\"},{\"type\":1,\"output\":\"** testing if installed package can be loaded from final location\\r\\n\"},{\"type\":1,\"output\":\"\"},{\"type\":1,\"output\":\"** testing if installed package keeps a record of temporary installation path\\r\\n\"},{\"type\":1,\"output\":\"\"},{\"type\":1,\"output\":\"* DONE (nanotatoR)\\r\\n\"},{\"type\":1,\"output\":\"\"}]"
                     -compile_pdf_state="{\"tab_visible\":false,\"running\":false,\"target_file\":\"\",\"output\":\"\",\"errors\":[]}"
                     -files.monitored-path=""
                     -find-in-files-state="{\"handle\":\"\",\"input\":\"\",\"path\":\"\",\"regex\":false,\"ignoreCase\":false,\"results\":{\"file\":[],\"line\":[],\"lineValue\":[],\"matchOn\":[],\"matchOff\":[],\"replaceMatchOn\":[],\"replaceMatchOff\":[]},\"running\":false,\"replace\":false,\"preview\":false,\"gitFlag\":false,\"replacePattern\":\"\"}"
                     -imageDirtyState="1"
                     -saveActionState="-1"

.Rproj.user/3F8D143E/rmd-outputs

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+                    -
+                    -
+                    -
+                    -
+                    -

.Rproj.user/3F8D143E/saved_source_markers

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                     -{"active_set":"","sets":[]}
                     \ No newline at end of file

.Rproj.user/3F8D143E/sources/prop/47696581

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                     -{
                     -    "source_window_id": "",
                     -    "Source": "Source"
                     -}
                     \ No newline at end of file

.Rproj.user/3F8D143E/sources/prop/INDEX

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@@ -1 +0,0 @@
                     -C%3A%2FSuro%2FnanotatoR%2FnanotatoR%2FR%2Fhello.R="47696581"

.Rproj.user/3F8D143E/sources/s-5E981E40/lock_file

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deleted file mode 100644

.Rproj.user/3F8D143E/vcs_options

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@@ -1 +0,0 @@
                     -activeVcsOverride="Git"

.Rproj.user/shared/notebooks/patch-chunk-names

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deleted file mode 100644

.Rproj.user/shared/notebooks/paths

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@@ -1 +0,0 @@
                     -C:/Suro/nanotatoR/nanotatoR/R/hello.R="2AC31D85"

R/OverlappingGenes.r

History View file @ 389978e

@@ -264,9 +264,6 @@ readSMap_DLE <- function(smap, smapdata,
                              } else {
                              stop("column names doesnot Match")
+                             }
                     -<<<<<<< HEAD
                     -        Samp <- as.character(unique(r1$Sample))
                     -=======
                      		if(any(unique(r1$Sample) == "ExperimentLabel") == TRUE){
                      	        g1 <- strsplit(smap, split = "/")
@@ -278,7 +275,6 @@ readSMap_DLE <- function(smap, smapdata,
                      	       	Samp <- as.character(unique(r1$Sample))
+                     	    }
                              #Samp <- as.character(unique(r1$Sample))
                     ->>>>>>> 290722e937d0be2298a6f67270fd541e2ee3ab6e
                              'st1 <- strsplit(Samp, split = "*_DLE")
                              SampleID <- st1[[1]][1]'
                              if(length(grep("*_BspQI_*", Samp)) >= 1){

man/hello.Rd

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                     -\name{hello}
                     -\alias{hello}
                     -\title{Hello, World!}
                     -\usage{
                     -hello()
                     -}
                     -\description{
                     -Prints 'Hello, world!'.
                     -}
                     -\examples{
                     -hello()
                     -}