d3b-center/annofuse

Filter and prioritize fusion calls

annofuse's Issues

Examples to showcase the usage of functions

Full set of examples for the functions exported

• aggregate_fusion_calls
• annoFuse_single_sample
• annotate_fusion_calls
• called_by_n_callers
• expression_filter_fusion
• fusion_driver
• fusion_filtering_QC
• fusion_multifused
• fusion_standardization
• get_Pfam_domain
• groupcount_fusion_calls
• plot_breakpoints
• plot_recurrent_fusions
• plot_recurrent_genes
• plot_summary
• report_fuse
• samplecount_fusion_calls
• shiny_fuse
• theme_publication
• zscored_annotation

Bug: First function "fusion_standardization" not working for star_fusion input

Provide the command used or report the bug here

star_fusion example run

star_fusion_calls <- read.csv("NTRK_control.star-fusion.fusion_predictions.abridged.tsv", sep="\t")
fusion_standardization(
  fusion_calls=star_fusion_calls,
  caller = c("STARFUSION"),
  tumorID = "NTRK_control"
)

What version are you using?

Most recent version as of Dec 17 2020

Add error message here (if applicable)

See attached screenshot

Add Session info

Run sessionInfo() and post the output below
R version 4.0.2 (2020-06-22)
Platform: x86_64-apple-darwin19.5.0 (64-bit)
Running under: macOS Catalina 10.15.7

Matrix products: default
BLAS: /System/Library/Frameworks/Accelerate.framework/Versions/A/Frameworks/vecLib.framework/Versions/A/libBLAS.dylib
LAPACK: /usr/local/Cellar/openblas/0.3.10_1/lib/libopenblasp-r0.3.10.dylib

locale:
[1] en_CA.UTF-8/en_CA.UTF-8/en_CA.UTF-8/C/en_CA.UTF-8/en_CA.UTF-8

attached base packages:
[1] grid stats graphics grDevices
[5] utils datasets methods base

other attached packages:
[1] data.table_1.13.2 stringr_1.4.0
[3] arsenal_3.5.0 annoFuse_0.90.0
[5] dplyr_1.0.1 ggrepel_0.8.2
[7] kableExtra_1.1.0 knitr_1.29
[9] ggplot2_3.3.2

loaded via a namespace (and not attached):
[1] readxl_1.3.1
[2] backports_1.1.8
[3] BiocFileCache_1.12.1
[4] plyr_1.8.6
[5] lazyeval_0.2.2
[6] shinydashboard_0.7.1
[7] BiocParallel_1.22.0
[8] usethis_1.6.3
[9] GenomeInfoDb_1.24.2
[10] digest_0.6.25
[11] ensembldb_2.12.1
[12] htmltools_0.5.0
[13] magick_2.4.0
[14] fansi_0.4.1
[15] magrittr_1.5
[16] memoise_1.1.0
[17] openxlsx_4.1.5
[18] remotes_2.2.0
[19] Biostrings_2.56.0
[20] readr_1.3.1
[21] matrixStats_0.57.0
[22] askpass_1.1
[23] prettyunits_1.1.1
[24] colorspace_1.4-1
[25] blob_1.2.1
[26] rvest_0.3.6
[27] rappdirs_0.3.1
[28] haven_2.3.1
[29] xfun_0.16
[30] callr_3.5.1
[31] crayon_1.3.4
[32] RCurl_1.98-1.2
[33] jsonlite_1.7.1
[34] glue_1.4.1
[35] gtable_0.3.0
[36] zlibbioc_1.34.0
[37] XVector_0.28.0
[38] webshot_0.5.2
[39] DelayedArray_0.14.1
[40] car_3.0-10
[41] pkgbuild_1.1.0
[42] BiocGenerics_0.34.0
[43] abind_1.4-5
[44] scales_1.1.1
[45] qdapRegex_0.7.2
[46] DBI_1.1.0
[47] ggthemes_4.2.0
[48] rstatix_0.6.0
[49] Rcpp_1.0.5
[50] viridisLite_0.3.0
[51] xtable_1.8-4
[52] progress_1.2.2
[53] foreign_0.8-80
[54] bit_4.0.4
[55] stats4_4.0.2
[56] DT_0.16
[57] htmlwidgets_1.5.1
[58] httr_1.4.2
[59] ellipsis_0.3.1
[60] pkgconfig_2.0.3
[61] XML_3.99-0.5
[62] farver_2.0.3
[63] dbplyr_1.4.4
[64] reshape2_1.4.4
[65] tidyselect_1.1.0
[66] labeling_0.3
[67] rlang_0.4.7
[68] later_1.1.0.1
[69] AnnotationDbi_1.50.3
[70] cellranger_1.1.0
[71] munsell_0.5.0
[72] tools_4.0.2
[73] cli_2.0.2
[74] generics_0.0.2
[75] RSQLite_2.2.0
[76] devtools_2.3.2
[77] rintrojs_0.2.2
[78] broom_0.7.3
[79] shinyBS_0.61
[80] evaluate_0.14
[81] fastmap_1.0.1
[82] yaml_2.2.1
[83] processx_3.4.4
[84] bit64_4.0.2
[85] fs_1.5.0
[86] shinycssloaders_1.0.0
[87] zip_2.1.0
[88] purrr_0.3.4
[89] AnnotationFilter_1.12.0
[90] mime_0.9
[91] xml2_1.3.2
[92] biomaRt_2.44.1
[93] compiler_4.0.2
[94] shinythemes_1.1.2
[95] rstudioapi_0.11
[96] curl_4.3
[97] EnsDb.Hsapiens.v86_2.99.0
[98] testthat_2.3.2
[99] ggsignif_0.6.0
[100] tibble_3.0.3
[101] stringi_1.4.6
[102] highr_0.8
[103] ps_1.3.3
[104] GenomicFeatures_1.40.1
[105] desc_1.2.0
[106] forcats_0.5.0
[107] lattice_0.20-41
[108] ProtGenerics_1.20.0
[109] Matrix_1.2-18
[110] vctrs_0.3.2
[111] pillar_1.4.6
[112] lifecycle_0.2.0
[113] bitops_1.0-6
[114] httpuv_1.5.4
[115] rtracklayer_1.48.0
[116] GenomicRanges_1.40.0
[117] R6_2.4.1
[118] promises_1.1.1
[119] rio_0.5.16
[120] IRanges_2.22.2
[121] sessioninfo_1.1.1
[122] assertthat_0.2.1
[123] pkgload_1.1.0
[124] SummarizedExperiment_1.18.2
[125] openssl_1.4.2
[126] rprojroot_1.3-2
[127] withr_2.2.0
[128] GenomicAlignments_1.24.0
[129] Rsamtools_2.4.0
[130] S4Vectors_0.26.1
[131] GenomeInfoDbData_1.2.3
[132] parallel_4.0.2
[133] hms_0.5.3
[134] tidyr_1.1.2
[135] rmarkdown_2.3
[136] carData_3.0-4
[137] ggpubr_0.4.0
[138] Biobase_2.48.0
[139] shiny_1.5.0
[140] base64enc_0.1-3
[141] tinytex_0.25

breakpoint plots not showing up in dev branches

Branch: exemplary

Fusion breakpoint plots not displaying.

Warning in plot_breakpoints(domainDataFrame = breakpoints_info, exons = values$data_exons,  :
  FusionName not provide; using first row of domainDataFrame
Warning: Error in if: argument is of length zero
  [No stack trace available]

plot link broken

Plot link in the wiki (item 4) is broken.

cleanup of gene reference lists

• https://github.com/d3b-center/annoFuse/blob/master/inst/extdata/genelistreference.txt has rownames - remove
• https://github.com/d3b-center/annoFuse/blob/master/inst/extdata/fusionreference.txt has filenames but files not in repo; also has rownames -> add files? remove rownames
• add headers to files of gene/fusion files to add source info

Feature request: customizable plot summary

Purpose/implementation Section

Briefly descibe the feature

Add options to customize plot_summary ?
This topic came up while we reviewed output from a different project, if the user wants to gather summary for specific columns only for example if we should get distribution of fusion type per a user provided input ( maybe like subgroup) instead of fusion caller in the current top right corner.
Not sure if the pdf generated in the best option then maybe would need widget with column options and generic bar plots per column . This is up for discussion so adding @jharenza for input

Who will complete the feature request (please add a GitHub handle here if relevant)?

develop by @kgaonkar6 and @jharenza for input

update shiny server url name

from annoFuse to shinyFuse

add info on shiny server about file input requirements

This can go in the About section

add text for "about" info in shiny app

Hi @federicomarini - this is a quick writeup of some of the things we can add to the text boxes.

I think we can have 2 sections in About, then News, in a separate tab, and Contact in another tab, if possible.

About FusionExplorer

FusionExplorer is an interactive way to explore the putative oncogenic fusion results from annoFuse.
Required input: PutativeOncogenicFusion.tsv
Features:
Filtering: Select a column and enter one or more attributes on which to filter the rows.
Data export: Export the filtered table using the download button above.
Fusion visualization: To view the gene fusion, exons, protein domains, and breakpoints:

1. Load the exons and pfam domains by clicking the buttons on the upper right side.
2. Select any row in the data table to visualize that specific fusion. Plots for the 5' gene, 3' gene, and both genes will be generated to the right of the table.

Plot export: To save the fusion plot, select the green download arrow below the plot.

About FusionSummary

Features:
Recurrent fusions: To analyze recurrent fusions within a cohort:

1. To the left of the table, select a Grouping Column. This will be the column used for analysis of recurrent fusions. For example, if your dataset has multiple histologies and you are interested in recurrent fusions by histology, this value would be histology.
2. Select the number of top fusions to display in the plot.
3. Select a Counting column. This is usually a patient-level identifier.

Fusion visualization: To view the recurrent fusions results, click on the FusionSummary tab, where plots for recurrent fusions and recurrently-fused genes will be generated.
Plot export: To save the fusion plot, select the green download arrow below the plot.

News

[Date of Launch]. Welcome to ShinyFuse, an application for exploration of fusion output derived from annoFuse! The purpose of this application is Please take the tour, activated by clicking on the question mark in the upper right corner, and test out the demo dataset by clicking on Load demo data in the upper left corner. Thanks for visiting!

Contact

Please file application issues, suggestions, or bug reports here.

Update feature: annoFuse summary plot in shiny

Purpose/implementation Section

Briefly descibe the feature

I was wondering if we should allow users to provide the grouping column for plot_summary() call here:

annoFuse/R/shinyFuse.R

Line 799 in 92cdd69

p <- plot_summary(values$annofuse_tbl, base_size = 10)

currently it uses the default groupby <- "Sample" looks quite busy when we have a lot of samples.

Can we add groupby=gby_rf to the function call to use the reactive value from the user as we do for the recurrent plots? This would be useful when the user has subgroup columns like we had "broad_histology" to plot fusion summary and recurrent fusion/gene per subgroup which might look cleaner.

Who will complete the feature request (please add a GitHub handle here if relevant)?

@federicomarini

novel promoter swap from gene fusion

From @jharenza regarding reviewer's comment:

How the authors handle the annotation of fusions if they don't necessarily fall in exon-exon boundaries? For example in MALAT1-GLI1 fusions, the break happens in the middle of the gene body of MALAT1 (a non-coding gene) and the break on the GLI1 can happen some bases upstream on exon 5-6. Would an important fusion like be annotated correctly and not filtered away? How would you classify this fusion since it is not "in-frame" (there is no frame on the MALAT1, since it is non-coding)?  Would it provide some annotation saying that is likely a "promoter-swap" kind of event? I understand most fusions occur in exons borders but I would like to know if this tool is able to handle interesting real biology cases like the one described

Can we add some annotation saying that a fusion is likely to be a "promoter-swap" kind of event?

For this and similar fasta sequence(epitope etc) analysis standard fusion format will also need to extract fusion sequence from caller input

rename shinyFuse table download

What data file(s) does this issue pertain to?

shinyFuseshinyfuse.csv download table from shinyFuse

What version are you using?

v0.90.0

Put your question or report your issue here.

Rename output tables to something more descriptive like shinyFuseFusionTable.csv (?)

table summary errors

Branches tested: loading_progress and exemplary

Insufficient values in manual scale. 6 needed but only 3 provided.

and

Insufficient values in manual scale. 4 needed but only 3 provided.` are errors when doing grouping.

Perhaps also rename TableSummary to Recurrent Fusions and TableExplorer to Fusion Explorer.

@federicomarini

dependency error

See below when trying to install via GitHub:

library(devtools)
install_github("d3b-center/annoFuse")

ERROR: dependency ‘EnsDb.Hsapiens.v86’ is not available for package ‘annoFuse’

• removing ‘/Library/Frameworks/R.framework/Versions/3.6/Resources/library/annoFuse’
  Error: Failed to install 'annoFuse' from GitHub:
  (converted from warning) installation of package ‘/var/folders/zs/8g7y6mfs7lldb27t4w906hj1z51wzr/T//RtmpwBuHpZ/filefae15df1672f/annoFuse_0.2.tar.gz’ had non-zero exit status

Add templates for issues and PRs

Add templates for issues and PRs - model after OpenPBTA analysis?

Function to annotate fusion calls from Arriba

Hello,

Thanks for this useful resource.

I am trying to find ways to use annoFuse for our internal RNAseq samples.
We use bcbio-RNAseq pipeline for the processing of samples in a single sample setting. Also, our focus is on the fusion calls from Arriba.

I was thinking of starting with annotate_fusion_calls function to annotate Arriba calls and then later apply prioritisation. However, I have few questions;

• Would it be reasonable to use annoFuse on a single sample fusion calls? Or the tool is more useful for cohort based analysis? From the annoFuse paper it seems you had tested the tool on a cohort of samples from OpenPBTA project.

• If yes - can you please clarify what is expected as input for geneListReferenceDataTab and fusionReferenceDataTab in the annotate_fusion_calls function? I could not figure this out from the description in the man page. Can you please share any examples?

This will be much appreciated.

---

Sehrish K

Quick numeric summary returned after processing files

Idea: to have a quick numeric summary returned after processing files

Rationale: often one might overlook what happened and "just takes" the output. Exposing a compact summary of what was retained/filtered out can help to be aware of parameter values.

Implementation: could be a combination of message calls, that e.g. can be printed out to console without messing around with the returned output 😉

domain plots and recurrence plots for shiny_fuse

Description

General issue:
Updates for plots for use in shiny_fuse and app

Specifics:
Domain plots

• add domain legend to the bottom ( internal to annoFuse )
• add filtering inside the plot_breakpoint()
• add Sample param to plot_breakpoint()
• if non-coding genes in fusion add just exon gene structure and if intergenic add genomic in x axis
• if plotting breakpoints across Samples then need to have interactive pop up of Sample name when the user hovers over the line (to-do for later)

Recurrent fusion/genes plots:

• bigger x axis labels ( internal to annoFuse )
• titles for plots ( internal to annoFuse )
• these plots for recurrent plots/ summary plot need grouping variable, we need to discuss ways to have that information added/provided in the app/shiny_fuse function (shiny_fuse)
• fix xlim on right plot
• right plot legend - move to bottom

How will work on this:
@kgaonkar6 will work on the topics which are "internal to annoFuse" functions
@federicomarini can take a look at the "shiny_fuse" specific tasks

add kinase domain retention info to putative oncogenic file

add kinaseGeneDomainRetained and rename GeneLoc -> kinaseDomainGeneLoc

update breakpoint plots

• Add by row functionality
• Make plots landscape for printing
• Make plot of both right/left larger for better export.

update conjoin genes filter

Remove this filter

additional column features for FusionExplorer

Few suggestions:

• Freeze header row and create scroll bar within table instead of on entire app page
• Enable the user to select only columns of interest for viewing / remove columns that are bulking up the table

Bug: issue loading tidyr::one_of()

Provide the command used or report the bug here

What version are you using?

Add error message here (if applicable)

@federicomarini @jharenza
It seems annoFuse imports tidyr::one_of() which was only added to tidyr1.02 or later but we have tidyr0.8.3 in openpbta docker so I was trying to update the version but without luck.

I think changing the @importFrom to dplyr::one_of() fixed the issue while loading annoFuse in openPBTA docker

Add Session info

Run sessionInfo() and post the output below

large files pfambioMart and exon

Add function to only generate the pfambioMart and exon once when needed within the package.

filter dropdown for BreakpointLocation

Description

@federicomarini can we add BreakpointLocation as a filter?

Basically by doing the following filters using the demo file we will be able to reproduce the figure in the MS.

sfc <- as.data.frame(sfc[ which(sfc$Fusion_Type == "in-frame" & sfc$BreakpointLocation == "Genic"),])
before runnning
plot_recurrent_genes(sfc, groupby = "broad_histology", countID = "Kids_First_Participant_ID")

@jharenza should we also make BreakpointLocation a standard fusion call column applicable so that the filter is applicable to all annoFuse output?

filtering list for shiny app

Be able to filter prior to plotting:

• Fusion_Type
• caller.count
• SpanningFragCount
• Confidence
• Caller

update intergenic logic

Seeing instances of intergenic gene fusions being called intragenic in V16:

BS_03FT4S8B: LINC01019--LINC01019/IRX1
BS_7ZV3DPGT: CNTN6--CNTN6/RPL23AP38

Comparing the intergenic annotations to these, it seems that these are being called intragenic due to the fact that Gene1A and Gene1B are identical.

If all intergenic fusions will always have a /, then I suggest simple logic built around that.

cleanup DS_store and license files

Delete DS_store and remove one of the license files
Rproj.user folder needs to be removed
Clean up doc and build vignettes from them

possibly make spanning difference an option

Depending on results of comparison between TCGA and PBTA, and potentially another longread dataset with high confidence fusion calls, we can make this an option with default filtering turned on (could make this by read length or not - need to inspect fusion calls in PBTA for false +).

• @kgaonkar6 Add SpanningDelta to standardFusioncalls

add support for hg19

I found pcawg fusion dataset (hg19)
standardFusioncalls_pcawg.txt
https://dcc.icgc.org/releases/PCAWG/transcriptome/fusion

Just wanted to add here that the hg19 support is mostly important because published PCAWG/DKFZ workflows are hg19 based.

Note: It's already filtered I didn't find raw calls
This resulted in detection of 3540 fusion events, from these 2268 were detected by
both FusionCatcher/STAR-Fusion and FusionMap (from these 1821 had SV support)
and 1112 were detected by only one method and had SV support. All fusions are
available in Synapse (syn10003873)

Works for most plot except plot_breakpoints since the exon RDS is based on hg38
For example the RET gene location are as follows
chr10:43,077,027-43,130,351(GRCh38/hg38)
chr10:43,572,475-43,625,799(GRCh37/hg19)

So using the current exon RDS file the breakpoint is outside the genebody

Gene1A	Gene1B	RightBreakpoint	LeftBreakpoint
CCDC6	RET	10:61665880	10:43612032

Unable to standardize starfusion calls

Hi there, this looks to be an excellent tool, I am hoping I can get it to work!

This is the command I am trying:

standardizedSTARfusion<-fusion_standardization(fusion_calls = ST.STARFusion, caller = "STARfusion")

I do see that caller string options are STARfusion/arriba

#ERROR
Error in fusion_standardization(fusion_calls = ST.STARFusion, caller = "STARfusion") :
STARfusion is not a supported caller string.

I would also like some clarity on the workflow, I have calls from Arriba and STARfusion, I would like to merge the calls and prioritze the calls. Is this done after standardizing and what is the command for that.

I was also not able to run Fusion annototor on Arriba output, is this done after standardization?

update default columns to display in shinyFuse

Let's use these:

Sample
FusionName
LeftBreakpoint
RightBreakpoint
Fusion_Type
JunctionReadCount
SpanningFragCount
Confidence
CalledBy

source R script names to represent function calls

Description

General issue:
R score file names and functions don't match up

Specifics:
plotRecurrentFusion is in plot_recurrent_fusion.R
plotRecurrentGenes is in plot_recurrent_genes.R
plotBreakpoints is in 'plot_breakpoints.R fusion_multifusedis infusionMultifused.R annotate_fusion_callsis inannotate_fusion.R expressionFilterFusionis inexpression_filtering.R`

Styler for all scripts

All functions to be in snake_case as per discussion below

How will work on this
@federicomarini will work on changing the names in the code
@kgaonkar6 to update the Fig1 function names

add junctionreadcount to plot filter

For some reason, this got removed

breakpoint plots - some error out

Branch: takeatour

Some rows error out and default back to plotting multiple breakpoints. For example: sample BS_17WYVEEC KIAA1549--BRAF fusion gives error:

Warning: Error in plot_breakpoints: domainDataFrame is empty after selecting for fusionname 
  [No stack trace available]

and plot:

annofuse_bpboth.pdf

Related: the plot render here is smushed. @kgaonkar6

add compatibility with other fusion tools

Suggestions (all may not be feasible) - edit where necessary @kgaonkar6

• deFuse
• FusionCatcher
• Jaffa
• SOAPFuse

Bug: missing ref files and shinyFuse demo file

Provide the command used or report the bug here

Was searching for our demo data (putative oncogenic file we use for shinyfuse) and noticed it, along with the reference folder are missing.

What version are you using?

Current master

Add error message here (if applicable)

NA

Add Session info

Run sessionInfo() and post the output below
NA

download table not working

When I try to download the table, I get an RStudio popup but no table being saved.

Also, I noticed that when I try to copy to clipboard after filtering, say, for in-frame fusion_type, it only copies the visible rows (25) instead of the true selection (1,613) of 4,462. In addition to this, when pasting, the output does not paste properly because of blank cells. Maybe we remove copy altogether right now?

opt in annoFuseSingleSample

Description

leftover testing opt_args in annoFuseSingleSample function needs to be removed

@kgaonkar6 will work on this

tcga validation nb and files

Add TCGA validation nb and files as vignette

Bug: annoFuse::annoFuse_single_sample with no filtered fusion calls errors out

Provide the command used or report the bug here

What version are you using?

Add error message here (if applicable)

https://cavatica.sbgenomics.com/u/kfdrc-harmonization/sd-bhjxbdqk-ad-hoc-annofuse/tasks/a5fc74b3-da0e-4683-ad2d-4298f1469d8f/stats/
2021-01-06T12:41:57.101146919Z 4: In fusion_filtering_QC(standardFusioncalls = standardFusioncalls, :
2021-01-06T12:41:57.101151409Z No fusion calls with readingframe: in-frameNo fusion calls with readingframe: frameshift
2021-01-06T12:41:57.101155305Z Execution halted

It seems no fusion call has atleast 1 junction read to support the fusion so in fusion_filtering_QC no fusion calls are left as output.

Add Session info

Run sessionInfo() and post the output below
Was run on cavatica

minor column name fixes

Minor column name suggestion to standardize. Eg:
caller.count is the only column name with a period in it
Some columns have no underscore between words, and some do

Example data for shiny_fuse

I've added v16 version of PutativeDriverAnnoFuse files here https://github.com/d3b-center/annoFuse/tree/add_v16_files/inst/extdata

This file needs to be filtered :
Filter clinical columns to only integrated_diagnosis and broad_histology
Add BreakpointLocation column with values "Genic","Intergenic" and "Intragenic"

And renamed to just PutativeDriverAnnoFuse.tsv to be used in all examples and shiny_fuse demo data

update instructions for filtering of numeric columns

Sliding scales currently, hard to select 1 number for filtering, but can be achieved by 10 … 10

Road to Bioc

Here's a list of items that likely will need to be addressed if we want annoFuse included in Bioconductor

• expand the vignettes (e.g. nice ideas could come from the current doc folder)

• roxygen to fully document the package and precisely specifying importFrom commands

• examples to showcase the usage of functions

• a NEWS.md file would not hurt?

• specification of some biocViews to define the "landing area"

• link to some potential output files to use as showcasing? (could be then plugged in e.g. into the shiny app)

• version number to be adjusted (0.99.0 for submission

• related to the examples - it is a nice thing if we had unit tests, would make the code pretty robust to the nasty edge cases 😃

We could split them up to single issues for easier tracking, if desired!
Federico

spanningDelta cutoff 100 for demo file

@kgaonkar6

• update the demo file used in shiny_app to have cutoff of 100 (@federicomarini if I keep the file name the same in extdata it won't require any changes from your side right? )
• update default cutoff 100 in filter_fusion_QC function
• update plots with spanningdelta 100 cutoff for main figure

Internal function to check for standardized columns for plots

Description

Internal check for files that are provided as input in shiny_fuse or plots and other functions in general just 1 to check all columns.

Specifics

For domain plots basic columns are "LeftBreakpoint", "RightBreakpoint", "FusionName", "Gene1A" and "Gene1B"
For recurrent plots and summary plot the basic columns are "LeftBreakpoint", "RightBreakpoint", "FusionName", "Gene1A" and "Gene1B" and a "grouping variable"
For filtering_fusion_QC the basic columns are "LeftBreakpoint" , "RightBreakpoint" , "FusionName" , "Sample" , "Caller" , "Fusion_Type" , "JunctionReadCount" , "SpanningFragCount" , "annots"

• @kgaonkar6 Make "Sample" column as user provided ID in annofuse_single_sample and formt_calls functions
• @kgaonkar6 to check if all columns as read as characters or numeric in input_files

How will work on this
@federicomarini has added an internal function to check and add message if it correct input file.

filtering on shiny server

Not sure how to fix this aside from a dropdown, but for instance in the new BreakpointLocation column, when searching for Genic, all 3 values: Genic, Intergenic, and Intragenic come up in the FusionExplorer, due to the match of genic in each term. Thoughts, @federicomarini ?

add shinyFuse launch date

In the About section, add 2020-09-18 as the release date!

add authors to package

Update description with package authors:

Authors@R: c(person("Krutika", "S.", "Gaonkar", role = c("aut", "cre"),
email = "[email protected]",
comment = c(ORCID = "0000-0003-0838-2405")),
person("Federico", "Marini", role = "aut",
email = "[email protected]",
comment = c(ORCID = "0000-0003-3252-7758")),
person("Komal", "S.", "Rathi", role = "ctb",
email = "[email protected]",
comment = c(ORCID = "0000-0001-5534-6904")),
person("Jaclyn", "N.", "Taroni", role = "ctb",
email = "[email protected]",
comment = c(ORCID = "0000-0003-4734-4508")))

@federicomarini - I switched you from ctb to aut because using this guidance, you had substantial contributions with shinyFuse and reportFuse.