Implement a function PlotRelStartStopDistance to show the distribution of sites relative to the start/stop codon in a function ; this would parallel the other distance/enrichment functions:

PlotSectionDistribution and PlotSectionEnrichment
PlotSpatialDistribution and PlotSpatialEnrichment
PlotRelDistDistribution and PlotRelDistDistribution

> BuildTx("hg38")
Building the transcriptome. This will take a few minutes.
Note that this step should only be done once.
[Fri Feb 10 2017 09:59:57] Stage 1/6: Checking package dependencies.
[Fri Feb 10 2017 09:59:57] Stage 2/6: Getting transcripts and gene annotations.
Download the refGene table ... OK
Download the hgFixed.refLink table ... OK
Extract the 'transcripts' data frame ... OK
Extract the 'splicings' data frame ... OK
Download and preprocess the 'chrominfo' data frame ... OK
Prepare the 'metadata' data frame ... OK
Make the TxDb object ... OK
'select()' returned 1:1 mapping between keys and columns
'select()' returned 1:many mapping between keys and columns
'select()' returned 1:many mapping between keys and columns
'select()' returned 1:1 mapping between keys and columns
[Fri Feb 10 2017 10:07:47] Stage 3/6: Splitting transcripts by section.
[Fri Feb 10 2017 10:08:07] Stage 4/6: Collapsing isoforms.
Collapsing duplicate 5'UTR entries
Error: 'elementLengths' is defunct.
Use 'elementNROWS' instead.
See help("Defunct")
In addition: Warning messages:
1: In .extractCdsLocsFromUCSCTxTable(ucsc_txtable, exon_locs) :
UCSC data anomaly in 571 transcript(s): the cds cumulative length is
not a multiple of 3 for transcripts ‘NM_001305275’ ‘NM_017940’
‘NM_001289974’ ‘NM_001291281’ ‘NM_001134939’ ‘NM_001301371’
‘NM_016178’ ‘NM_001348286’ ‘NM_001145051’ ‘NM_001128929’ ‘NM_001075’
‘NM_001144767’ ‘NM_001348208’ ‘NM_001322371’ ‘NM_032470’ ‘NM_032454’
‘NM_004197’ ‘NM_016098’ ‘NM_001788’ ‘NM_015068’ ‘NM_001184961’
‘NM_001172437’ ‘NM_001159995’ ‘NM_001159999’ ‘NM_001160001’
‘NM_004408’ ‘NM_001288737’ ‘NM_001288739’ ‘NM_001288738’
‘NM_001005336’ ‘NM_020469’ ‘NM_001001676’ ‘NM_033380’ ‘NM_002457’
‘NM_053005’ ‘NM_001348221’ ‘NM_001013356’ ‘NM_001348230’ ‘NM_173600’
‘NM_006400’ ‘NM_001130048’ ‘NM_001318849’ ‘NM_015296’ ‘NM_001348266’
‘NM_006220’ ‘NM_001282494’ ‘NM_001282490’ ‘NM_001301302’ ‘NM_002537’ [... truncated]
2: RSQLite::dbGetPreparedQuery() is deprecated, please switch to DBI::dbGetQuery(params = bind.data).
3: Named parameters not used in query: internal_chrom_id, chrom, length, is_circular
4: Named parameters not used in query: internal_id, name, type, chrom, strand, start, end
5: Named parameters not used in query: internal_id, name, chrom, strand, start, end
6: Named parameters not used in query: internal_id, name, chrom, strand, start, end
7: Named parameters not used in query: internal_tx_id, exon_rank, internal_exon_id, internal_cds_id
8: Named parameters not used in query: gene_id, internal_tx_id

> sessionInfo()
R version 3.3.1 (2016-06-21)
Platform: x86_64-redhat-linux-gnu (64-bit)
Running under: Red Hat Enterprise Linux Server release 6.8 (Santiago)

locale:
[1] LC_CTYPE=en_NZ.UTF-8 LC_NUMERIC=C
[3] LC_TIME=en_NZ.UTF-8 LC_COLLATE=en_NZ.UTF-8
[5] LC_MONETARY=en_NZ.UTF-8 LC_MESSAGES=en_NZ.UTF-8
[7] LC_PAPER=en_NZ.UTF-8 LC_NAME=C
[9] LC_ADDRESS=C LC_TELEPHONE=C
[11] LC_MEASUREMENT=en_NZ.UTF-8 LC_IDENTIFICATION=C

attached base packages:
[1] parallel stats4 stats graphics grDevices utils datasets
[8] methods base

other attached packages:
[1] TxDb.Hsapiens.UCSC.hg38.knownGene_3.4.0
[2] BiocInstaller_1.24.0
[3] org.Hs.eg.db_3.4.0
[4] RNAModR_0.1.0
[5] GenomicFeatures_1.26.2
[6] AnnotationDbi_1.36.2
[7] Biobase_2.34.0
[8] GenomicRanges_1.26.2
[9] GenomeInfoDb_1.10.3
[10] IRanges_2.8.1
[11] S4Vectors_0.12.1
[12] BiocGenerics_0.20.0

loaded via a namespace (and not attached):
[1] Rcpp_0.12.9 XVector_0.14.0
[3] zlibbioc_1.20.0 GenomicAlignments_1.10.0
[5] beanplot_1.2 BiocParallel_1.8.1
[7] lattice_0.20-33 caTools_1.17.1
[9] tools_3.3.1 grid_3.3.1
[11] SummarizedExperiment_1.4.0 KernSmooth_2.23-15
[13] DBI_0.5-1 gtools_3.5.0
[15] digest_0.6.12 Matrix_1.2-6
[17] rtracklayer_1.34.1 bitops_1.0-6
[19] RCurl_1.95-4.8 biomaRt_2.30.0
[21] memoise_1.0.0 RSQLite_1.1-2
[23] gdata_2.17.0 gplots_3.0.1
[25] Biostrings_2.42.1 Rsamtools_1.26.1
[27] XML_3.98-1.5

On R 3.6.1, Bioconductor version 3.9

BuildTx("hg38")
Building the transcriptome. This will take a few minutes.
Note that this step should only be done once.
...
Download the refGene table ... Error in result_fetch(res@ptr, n = n) : Error fetching buffer:
OK

This may be a problem with RMariaDB, with a similar error reported here.

GetEEJunct(refGenome = "hg38", filter = "CDS")
Error in (function (classes, fdef, mtable) :
unable to find an inherited method for function ‘psetdiff’ for signature ‘"GRangesList", "GRangesList"’

Hi,
It's a very useful tool for mRNA modification analysis!
I want to generate a metagene density plot like the paper in https://bmcbiol.biomedcentral.com/articles/10.1186/s12915-020-00769-5, This paper seems to use RNAModR for mRNA analysis too, but I don't know how to do it. Could you give me some advice?

Thanks in advance!
Best,
Qianzhao

Allow for variable/non-symmetric window sizes in

• Start/Stop codon enrichment analysis PlotRelStartStopEnrichment
• Distribution and enrichment of relative distances PlotRelDistDistribution and PlotRelDistEnrichment.

> PlotSpatialEnrichment(posSites, negSites, binWidth = 20, posMax = 1000)
Error in locNeg[[i]]$REGION_TXWIDTH - locNeg[[i]]$TXSTART :
non-numeric argument to binary operator

> PlotOverlap(posSites, negSites)
Error in .normargSEW0(start, "start") :
'start' must be a numeric vector (or NULL)

> PlotGC(posSites, negSites, flank = 10)
Error in rowSums(nucFreq[, c(2, 3)]) :
'x' must be an array of at least two dimensions

Reproducible minimal example:

library(RNAModR)
library(magrittr)
m1A <- system.file("extdata", "MeRIPseq_m1A_Dominissini2016_hg38.bed", package = "RNAModR") %>%
    ReadBED() %>%
    SmartMap(id = "m1A", refGenome = "hg38") %>%
    FilterTxLoc(filter = c("5'UTR", "CDS", "3'UTR"))
null <- GenerateNull(m1A, method = "ntAbund", nt = "A")

PlotSpatialEnrichment(m5C, null, binWidth = 100, posMax = 400)
Error in seq.default(1, length(x1), deltaIdx) : invalid '(to - from)/by'

The following works

PlotSpatialEnrichment(m5C, null, binWidth = 80, posMax = 400)

Hi,

I'm not sure about how to use the GetEEJunct and PlotRelDistDistribution funtions.

I test this using the system file miCLIP_m6A_Linder2015_hg38.bed and bsRNAseq_m5C_Squires2012_hg38.bed. And the transcriptome data was downloaded from https://drive.google.com/file/d/0B5_hfxBdKWHRVlBCTUlSazJfaWs/view

Codes:
source("http://www.bioconductor.org/biocLite.R")
biocLite(c("AnnotationDbi", "beanplot", "Biostrings", "GenomeInfoDb", "GenomicFeatures", "GenomicRanges", "gplots", "RSQLite", "rtracklayer"))

biocLite(c("BSgenome.Hsapiens.UCSC.hg38", "org.Hs.eg.db"))

if (!require("devtools")) install.packages("devtools"); devtools::install_github("mevers/RNAModR", build_vignettes = FALSE)

Load the library.

library(RNAModR)
library(RMariaDB)

Build reference transcriptome.

This might take a few minutes.

#BuildTx("hg38")

bedFile <- system.file("extdata", "miCLIP_m6A_Linder2015_hg38.bed", package = "RNAModR")
sites <- ReadBED(bedFile)
posSites <- SmartMap(sites , id= "m6A" ,refGenome = "hg38" )

bedFile <- system.file("extdata",
"bsRNAseq_m5C_Squires2012_hg38.bed",
package = "RNAModR")
sites <- ReadBED(bedFile)
m5Csites <- SmartMap(sites, id= "m5C" ,refGenome = "hg38" )

Error:
PlotRelDistDistribution(posSites,miRNA)

Error: gr1 is not an object of type GRangesList.

junction <- GetEEJunct(refGenome = "hg38", filter = "CDS")
Error in (function (classes, fdef, mtable) :
unable to find an inherited method for function ‘psetdiff’ for signature ‘"CompressedGRangesList", "GRangesList"’

Please have a look. Thank you.