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fixed vignettes
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Aufiero committed Jul 12, 2019
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43 changes: 19 additions & 24 deletions vignettes/circRNAprofiler.R
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Expand Up @@ -7,17 +7,18 @@ source("render_toc.R")
## ---- toc, echo = FALSE--------------------------------------------------
render_toc("circRNAprofiler.Rmd")

## ---- echo=FALSE, out.width='70%', fig.align="center", fig.cap="\\label{fig:figs} Schematic representation of the circRNA analysis workflow implemented by circRNAprofiler. The grey boxes represent the 15 modules with the main R-functions reported in italics. The different type of sequences that can be selected are depicted in the dashed box. BSJ, Back-Spliced Junction."----
## ---- echo=FALSE, out.width='60%', fig.align="center", fig.cap="\\label{fig:figs} Schematic representation of the circRNA analysis workflow implemented by circRNAprofiler. The grey boxes represent the 15 modules with the main R-functions reported in italics. The different type of sequences that can be selected are depicted in the dashed box. BSJ, Back-Spliced Junction."----

knitr::include_graphics("./images/image1.png")

## ---- eval = FALSE-------------------------------------------------------
# if (!requireNamespace("BiocManager", quietly = TRUE))
# install.packages("BiocManager")
#
# BiocManager::install("devtools")
# library(devtools)
# devtools::install_github("Aufiero/circRNAprofiler", build_opts = c(""))
# BiocManager::install("circRNAprofiler")

## ---- eval = FALSE-------------------------------------------------------
# BiocManager::install("Aufiero/circRNAprofiler")

## ------------------------------------------------------------------------
library(circRNAprofiler)
Expand All @@ -28,17 +29,17 @@ library(ggplot2)
library(VennDiagram)
library(gridExtra)

## ---- echo=FALSE, out.width='50%', fig.align="center", fig.cap="\\label{fig:figs} Example of a project folder structure"----
## ---- echo=FALSE, out.width='45%', fig.align="center", fig.cap="\\label{fig:figs} Example of a project folder structure"----
knitr::include_graphics("./images/image2.png")

## ---- eval = FALSE-------------------------------------------------------
# initCircRNAprofiler(projectFolderName = "circRNAprofiler", predictionTools =
# initCircRNAprofiler(projectFolderName = "circRNAprofiler", detectionTools =
# "mapsplice")

## ---- eval = FALSE-------------------------------------------------------
# initCircRNAprofiler(
# projectFolderName = "circRNAprofiler",
# predictionTools = c("mapsplice", "nclscan", "circmarker")
# detectionTools = c("mapsplice", "nclscan", "circmarker")
# )

## ---- echo=FALSE---------------------------------------------------------
Expand Down Expand Up @@ -114,13 +115,13 @@ head(gtf)
# Alternatively put the gtf file in the project folder, then run:
# gtf <- formatGTF(pathToGTF = "gencode.V19.annotation.gtf")

## ---- eval= FALSE--------------------------------------------------------
# # Load the object containing the detected circRNAs
# data("backSplicedJunctions")
# head(backSplicedJunctions)
#
# # Alternatively run:
# # backSplicedJunctions <- getBackSplicedJunctions(gtf)
## ------------------------------------------------------------------------
# Load the object containing the detected circRNAs
data("backSplicedJunctions")
head(backSplicedJunctions)

# Alternatively run:
# backSplicedJunctions <- getBackSplicedJunctions(gtf)

## ---- fig.align="center", fig.width = 10, fig.height = 3-----------------
# Plot
Expand Down Expand Up @@ -192,6 +193,7 @@ p <- VennDiagram::draw.triple.venn(
)



## ------------------------------------------------------------------------
# Compare condition B Vs A
deseqResBvsA <-
Expand Down Expand Up @@ -270,7 +272,7 @@ ggarrange(p1,
# head(edgerResCvsA)

## ---- eval = FALSE-------------------------------------------------------
# liftedBSJCoords <- liftBSJCoords(filteredCirc, map = "hg19ToMm9",
# liftedBSJcoords <- liftBSJcoords(filteredCirc, map = "hg19ToMm9",
# annotationHubID = "AH14155")

## ------------------------------------------------------------------------
Expand Down Expand Up @@ -441,7 +443,7 @@ genome <- BSgenome::getBSgenome("BSgenome.Hsapiens.UCSC.hg19")
knitr::include_graphics("./images/image4.png")

## ---- eval = FALSE-------------------------------------------------------
# # Type p[[3]] to get table
# # Type p[[3]] to get the table
# head(p[[3]])

## ----eval = FALSE--------------------------------------------------------
Expand All @@ -456,14 +458,7 @@ knitr::include_graphics("./images/image4.png")
#

## ----eval = FALSE--------------------------------------------------------
# rearragedMiRres <-
# rearrangeMiRres(
# miRsites,
# n = 40,
# color = "blue",
# miRid = TRUE,
# id = 1
# )
# rearragedMiRres <- rearrangeMiRres(miRsites)

## ---- eval=FALSE---------------------------------------------------------
# # If multiple circRNAs have been anlyzed for the presence of miR binding sites
Expand Down
195 changes: 103 additions & 92 deletions vignettes/circRNAprofiler.html
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Original file line number Diff line number Diff line change
Expand Up @@ -11,7 +11,7 @@

<meta name="author" content="Simona Aufiero" />

<meta name="date" content="2019-07-04" />
<meta name="date" content="2019-07-12" />

<title>circRNAprofiler: An R-based computational framework for the downstream analysis of circular RNAs</title>

Expand Down Expand Up @@ -192,7 +192,7 @@

<h1 class="title toc-ignore">circRNAprofiler: An R-based computational framework for the downstream analysis of circular RNAs</h1>
<h4 class="author">Simona Aufiero</h4>
<h4 class="date">2019-07-04</h4>
<h4 class="date">2019-07-12</h4>

</div>

Expand Down Expand Up @@ -585,6 +585,20 @@ <h4><em>getBackSplicedJunctions()</em></h4>
<pre class="r"><code># Load the object containing the detected circRNAs
data(&quot;backSplicedJunctions&quot;)
head(backSplicedJunctions)
## id gene strand chrom startUpBSE
## 1 ABHD2:+:chr15:89656956:89659752 ABHD2 + chr15 89656956
## 2 ACVR2A:+:chr2:148653870:148657467 ACVR2A + chr2 148653870
## 3 AFF1:+:chr4:87967318:87968746 AFF1 + chr4 87967318
## 4 AGTPBP1:-:chr9:88248289:88190230 AGTPBP1 - chr9 88248289
## 5 AGTPBP1:-:chr9:88248289:88200378 AGTPBP1 - chr9 88248289
## 6 AGTPBP1:-:chr9:88248289:88211277 AGTPBP1 - chr9 88248289
## endDownBSE tool C1 C2 C3 D1 D2 D3 H1 H2 H3
## 1 89659752 ms 35 11 38 48 38 12 34 44 41
## 2 148657467 ms 56 11 76 56 121 10 37 85 112
## 3 87968746 ms 47 5 34 48 47 5 54 10 30
## 4 88190230 ms 40 23 63 56 65 18 95 67 53
## 5 88200378 ms 13 3 19 26 43 7 20 32 23
## 6 88211277 ms 5 11 24 27 38 5 54 28 41

# Alternatively run:
# backSplicedJunctions &lt;- getBackSplicedJunctions(gtf)</code></pre>
Expand Down Expand Up @@ -915,20 +929,20 @@ <h4><em>getRandomBSJunctions()</em></h4>
randomBSJunctions &lt;-
getRandomBSJunctions(n = nrow(annotatedBSJs), f = f, gtf)
head(randomBSJunctions)
## id gene strand chrom startUpBSE
## 1 SLC8A1:-:chr2:40679209:40404892 SLC8A1 - chr2 40679209
## 2 N4BP2L2:-:chr13:33112962:33112755 N4BP2L2 - chr13 33112962
## 3 TECRL:-:chr4:65275116:65188405 TECRL - chr4 65275116
## 4 PICALM:-:chr11:85712184:85692172 PICALM - chr11 85712184
## 5 ALPK2:-:chr18:56246256:56212246 ALPK2 - chr18 56246256
## 6 ZNF91:-:chr19:23557566:23556544 ZNF91 - chr19 23557566
## id gene strand chrom startUpBSE
## 1 SYCP2:-:chr20:58487281:58476717 SYCP2 - chr20 58487281
## 2 PICALM:-:chr11:85780123:85733410 PICALM - chr11 85780123
## 3 INO80C:-:chr18:33077563:33076739 INO80C - chr18 33077563
## 4 PICALM:-:chr11:85711822:85692172 PICALM - chr11 85711822
## 5 MLIP-AS1:-:chr6:53905871:53893975 MLIP-AS1 - chr6 53905871
## 6 INO80C:-:chr18:33059375:33058246 INO80C - chr18 33059375
## endDownBSE
## 1 40404892
## 2 33112755
## 3 65188405
## 1 58476717
## 2 85733410
## 3 33076739
## 4 85692172
## 5 56212246
## 6 23556544</code></pre>
## 5 53893975
## 6 33058246</code></pre>
<p>Annotate randomly selected back-spliced junctions.</p>
<pre class="r"><code>annotatedRBSJs &lt;- annotateBSJs(randomBSJunctions, gtf, isRandom = TRUE)</code></pre>
<p>Use the plot functions to plot all the features of the annotated back-spliced-junctions.</p>
Expand Down Expand Up @@ -1238,36 +1252,35 @@ <h2>Note</h2>
## [8] datasets methods base
##
## other attached packages:
## [1] circRNAprofiler_0.99.9
## [2] BiocCheck_1.21.0
## [3] BSgenome.Hsapiens.UCSC.hg19_1.4.0
## [4] BSgenome_1.53.0
## [5] rtracklayer_1.45.1
## [6] Biostrings_2.53.0
## [7] XVector_0.25.0
## [8] gridExtra_2.3
## [9] VennDiagram_1.6.20
## [10] futile.logger_1.4.3
## [11] citr_0.3.0
## [12] knitr_1.23
## [13] rmarkdown_1.13
## [14] ggpubr_0.2
## [15] magrittr_1.5
## [16] ggplot2_3.2.0
## [17] gwascat_2.17.0
## [18] Homo.sapiens_1.3.1
## [19] TxDb.Hsapiens.UCSC.hg19.knownGene_3.2.2
## [20] org.Hs.eg.db_3.8.2
## [21] GO.db_3.8.2
## [22] OrganismDbi_1.27.0
## [23] GenomicFeatures_1.37.1
## [24] GenomicRanges_1.37.12
## [25] GenomeInfoDb_1.21.1
## [26] AnnotationDbi_1.47.0
## [27] IRanges_2.19.10
## [28] S4Vectors_0.23.13
## [29] Biobase_2.45.0
## [30] BiocGenerics_0.31.4
## [1] circRNAprofiler_0.99.13
## [2] BSgenome.Hsapiens.UCSC.hg19_1.4.0
## [3] BSgenome_1.53.0
## [4] rtracklayer_1.45.1
## [5] Biostrings_2.53.0
## [6] XVector_0.25.0
## [7] gridExtra_2.3
## [8] VennDiagram_1.6.20
## [9] futile.logger_1.4.3
## [10] ggpubr_0.2
## [11] magrittr_1.5
## [12] ggplot2_3.2.0
## [13] citr_0.3.0
## [14] knitr_1.23
## [15] BiocCheck_1.21.0
## [16] gwascat_2.17.0
## [17] Homo.sapiens_1.3.1
## [18] TxDb.Hsapiens.UCSC.hg19.knownGene_3.2.2
## [19] org.Hs.eg.db_3.8.2
## [20] GO.db_3.8.2
## [21] OrganismDbi_1.27.0
## [22] GenomicFeatures_1.37.1
## [23] GenomicRanges_1.37.12
## [24] GenomeInfoDb_1.21.1
## [25] AnnotationDbi_1.47.0
## [26] IRanges_2.19.10
## [27] S4Vectors_0.23.13
## [28] Biobase_2.45.0
## [29] BiocGenerics_0.31.4
##
## loaded via a namespace (and not attached):
## [1] backports_1.1.4 Hmisc_4.2-0
Expand All @@ -1283,54 +1296,52 @@ <h2>Note</h2>
## [21] blob_1.1.1 rappdirs_0.3.1
## [23] xfun_0.7 dplyr_0.8.1
## [25] jsonlite_1.6 crayon_1.3.4
## [27] RCurl_1.95-4.12 roxygen2_6.1.1
## [29] graph_1.63.0 genefilter_1.67.1
## [31] survival_2.44-1.1 glue_1.3.1
## [33] gtable_0.3.0 zlibbioc_1.31.0
## [35] seqinr_3.4-5 DelayedArray_0.11.2
## [37] scales_1.0.0 futile.options_1.0.1
## [39] DBI_1.0.0 edgeR_3.27.5
## [41] miniUI_0.1.1.1 Rcpp_1.0.1
## [43] xtable_1.8-4 progress_1.2.2
## [45] htmlTable_1.13.1 foreign_0.8-71
## [47] bit_1.1-14 Formula_1.2-3
## [49] getopt_1.20.3 htmlwidgets_1.3
## [51] httr_1.4.0 RColorBrewer_1.1-2
## [53] acepack_1.4.1 pkgconfig_2.0.2
## [55] XML_3.98-1.20 R.methodsS3_1.7.1
## [57] nnet_7.3-12 dbplyr_1.4.2
## [59] locfit_1.5-9.1 labeling_0.3
## [61] tidyselect_0.2.5 rlang_0.3.4
## [63] reshape2_1.4.3 later_0.8.0
## [65] biocViews_1.53.2 munsell_0.5.0
## [67] tools_3.6.0 RSQLite_2.1.1
## [69] ade4_1.7-13 evaluate_0.14
## [71] stringr_1.4.0 yaml_2.2.0
## [73] bit64_0.9-7 purrr_0.3.2
## [75] RBGL_1.61.0 mime_0.7
## [77] formatR_1.7 R.oo_1.22.0
## [79] xml2_1.2.0 biomaRt_2.41.3
## [81] compiler_3.6.0 rstudioapi_0.10
## [83] curl_3.3 interactiveDisplayBase_1.23.0
## [85] testthat_2.1.1 tibble_2.1.3
## [87] geneplotter_1.63.0 stringi_1.4.3
## [89] highr_0.8 desc_1.2.0
## [91] lattice_0.20-38 Matrix_1.2-17
## [93] commonmark_1.7 stringdist_0.9.5.2
## [95] pillar_1.4.1 RUnit_0.4.32
## [97] optparse_1.6.2 BiocManager_1.30.4
## [99] cowplot_0.9.4 data.table_1.12.2
## [101] bitops_1.0-6 httpuv_1.5.1
## [103] R6_2.4.0 latticeExtra_0.6-28
## [105] promises_1.0.1 codetools_0.2-16
## [107] lambda.r_1.2.3 MASS_7.3-51.4
## [109] assertthat_0.2.1 pkgload_1.0.2
## [111] SummarizedExperiment_1.15.4 DESeq2_1.25.1
## [113] rprojroot_1.3-2 withr_2.1.2
## [115] GenomicAlignments_1.21.3 Rsamtools_2.1.2
## [117] GenomeInfoDbData_1.2.1 hms_0.4.2
## [119] rpart_4.1-15 shiny_1.3.2
## [121] base64enc_0.1-3</code></pre>
## [27] RCurl_1.95-4.12 graph_1.63.0
## [29] genefilter_1.67.1 survival_2.44-1.1
## [31] glue_1.3.1 gtable_0.3.0
## [33] zlibbioc_1.31.0 seqinr_3.4-5
## [35] DelayedArray_0.11.2 scales_1.0.0
## [37] futile.options_1.0.1 DBI_1.0.0
## [39] edgeR_3.27.5 miniUI_0.1.1.1
## [41] Rcpp_1.0.1 xtable_1.8-4
## [43] progress_1.2.2 htmlTable_1.13.1
## [45] foreign_0.8-71 bit_1.1-14
## [47] Formula_1.2-3 htmlwidgets_1.3
## [49] httr_1.4.0 getopt_1.20.3
## [51] RColorBrewer_1.1-2 acepack_1.4.1
## [53] pkgconfig_2.0.2 XML_3.98-1.20
## [55] R.methodsS3_1.7.1 nnet_7.3-12
## [57] dbplyr_1.4.2 locfit_1.5-9.1
## [59] labeling_0.3 tidyselect_0.2.5
## [61] rlang_0.3.4 reshape2_1.4.3
## [63] later_0.8.0 munsell_0.5.0
## [65] biocViews_1.53.2 tools_3.6.0
## [67] RSQLite_2.1.1 ade4_1.7-13
## [69] evaluate_0.14 stringr_1.4.0
## [71] yaml_2.2.0 bit64_0.9-7
## [73] purrr_0.3.2 RBGL_1.61.0
## [75] mime_0.7 formatR_1.7
## [77] R.oo_1.22.0 xml2_1.2.0
## [79] biomaRt_2.41.3 compiler_3.6.0
## [81] rstudioapi_0.10 curl_3.3
## [83] interactiveDisplayBase_1.23.0 tibble_2.1.3
## [85] geneplotter_1.63.0 stringi_1.4.3
## [87] highr_0.8 lattice_0.20-38
## [89] Matrix_1.2-17 commonmark_1.7
## [91] stringdist_0.9.5.2 pillar_1.4.1
## [93] RUnit_0.4.32 optparse_1.6.2
## [95] BiocManager_1.30.4 cowplot_0.9.4
## [97] data.table_1.12.2 bitops_1.0-6
## [99] httpuv_1.5.1 R6_2.4.0
## [101] latticeExtra_0.6-28 promises_1.0.1
## [103] codetools_0.2-16 lambda.r_1.2.3
## [105] MASS_7.3-51.4 assertthat_0.2.1
## [107] SummarizedExperiment_1.15.4 DESeq2_1.25.1
## [109] withr_2.1.2 GenomicAlignments_1.21.3
## [111] Rsamtools_2.1.2 GenomeInfoDbData_1.2.1
## [113] hms_0.4.2 rpart_4.1-15
## [115] rmarkdown_1.13 shiny_1.3.2
## [117] base64enc_0.1-3</code></pre>
</div>
<div id="references" class="section level2 unnumbered">
<h2>References</h2>
Expand Down

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