.._add_datatype:

5. Extending Browse-R capabilities

5.1. Add a datatype handler

The Shiny Browse-R is easily customizable to show data from a new platform; all that is required is the addition of a platform-specific .R file in the code directory. For illustration, let us suppose we want to add a new datatype of 450K microarrays.

These steps will allow a new ‘datatype’ value to be specified in a dataset config file. In our example, let that datatype be “FourFiftyK”.

1. Create FourFiftyK.R in the data_types directory; the latter is at the same level with ui.R and server.R)

2. In FourFiftyK.R, create an R function, fetchData_base() with the following signature:

   fetchData_base <- function
   (
   pheno,          ##<<(data.frame) phenotype matrix
   selRange,       ##<<(GRanges) range being viewed on browser [start,end] - length 1
   bin_GR,         ##<<(GRanges) ranges of individual data bins
   numBins,        ##<<(integer) num. bins
   aggFUN=mean     ##<<(function) aggregating function
   ) {
           # fetch code goes here.
   
   ### (list with two keys):
   ### 1) coords: data.frame with three columns corresonding to the chromosome, start and end coordinate
   ### 2) values: sample-wise values. Row order should correspond to coords and column order to samples.
   

}

5.2. Current datatypes

5.2.1. bigwig

Used for any datatype which can be represented with a single column containing a continuous value.

5.2.2. BSseq

Used for bisulfite-seq data. Usually has two columns, M and COV, which are combined into a %methylation over an arbitrary genomic interval (e.g. in 2Kb bins, or over a gene).

Example view of input file:

Custom columns are: # CHROM_POS - columm # of sequence name in tabix file # START_POS - columm # of position start in tabix file # END_POS - column # of position end in tabix file # STRAND_POS - column # of strand # M_POS - column # of num. methylated cytosine (M) # COV_POS - column # of position coverage # minCov - minimum coverage to use

Computation is: (M/COV)

Future version will incorporate non-conversion rate subtraction capability.