FAQ

Q1. Can you tell me the naming convention for the genomic features?

I don't know what uc031tcg.1 is (but I do understand PCAT1, I think that naming convention is RefSeq, are the others also?).

A: I am trying to re-build gene symbols by collapsing transcripts into genes, when transcripts do not overlap with gene symbols, they get named as transcript names - in this case something like uc031tcg.1 - this is UCSC ID. See, udf_GeneSymbol for details. This part of the script is quite heavy and we are working on it.

Q2: Can you tell me how to interpret the wavy lines that cross the plot (for text in the figure legend)?

So far I am using this sentence: "The colored lines spanning the plotting region indicate the extent of LD for the lead SNPs with the same color designation, where the height of the line represents __ and the length of the line represents ___." Can you send me a better sentence to describe how these lines should be interpreted if I am not on the right track here?

A: It is a loess smoothing for matching hit SNP. If there are 2 SNPs marked with red and green shape and fill, then we will have 2 matching loess lines red and green. Smoothing is using LD values from 1000G phase EUR subset. We can use different cut-offs of LD: LD=0, LD > 0.1, LD >= 0.2, etc., usually LD = 0, i.e.: include all SNP LDs works best.

Y axis is 0 to 1, as in minimum and maximum value for LD - R^2. When wavy lines have similar shape, we can safely assume, those SNPs are the same signal. There is also an "R^2" track, the darker the lines the higher the LD, this track also helps visually see how hit SNPs overlap.

See Manhattan.R.

# LD smooth per hit SNP - optional
if("LDSmooth" %in% input$ShowHideTracks) {
  gg_out <- gg_out +
    geom_smooth(data=plotDatLD(),aes(x=BP,y=R2_Adj,col=LDSmoothCol),
                method="loess",se=FALSE)}

Q3. Can you tell me what is included (maybe even just the data source) for the histone and DNase panels?

What the colour interpretation is for the histone panel?

A: Data from ENCODE project, see links for more info.

• Histone - LocusExplorer README.md, UCSC tables

• DNaseI - LocusExplorer README.md, UCSC tables

Q4: Which operating system it is tested on?

A: See RSessionInfo.md

Q5: "Please download Histone bigWig files" message on the plot?

As GitHub has limitations on size of the repositories and files, Histone BigWig files are not included in LocusExplorer/Data/EncodeBigWig/. These files are public and can be downloaded from UCSC golden path - total ~2.5GB. Downloaded bigWig files must be saved in LocusExplorer/Data/EncodeBigWig/ folder.

We are working on server version of LocusExplorer, expected to be live by December 2015. Keep an eye on https://github.com/oncogenetics/LocusExplorer page. This will resolve the issues of different R versions. R packages, and no limits on anntation data - such as bigWig files.