iGD integration #37

joseverdezoto · 2020-03-31T23:05:58Z

Updated/Added scripts:

Added new script runLOLA_iGD.R updating the overlap calculations with IGDr.
Some minor changes to the loadPEPdb function to load the location of the iGD database as well as the index information (to properly order the overlap vector).

joseverdezoto and others added 29 commits October 21, 2019 16:07

function to create a list from a PEP object

7ef39b7

add code to load data as GRanges list

25f46eb

use readBED instead of fread

70ee370

take out ellipses in file path

8cb53c4

update description

ca44994

Delete readPEP.R

23d5797

add names to list elements

d7f7b53

Merge branch 'master' of github.com:joseverdezoto/LOLA

a93a5e5

preliminary annotation and config file for ucsc example

1323b15

add export and example

127efbb

add caching capability to loadPEPdb

3ca91b9

store cached regions next to annotation and config files

22bfcf2

fix simpleCache message

321b508

delete old version of the loadPEPdb function

f4828ec

change columns names to meet LOLA annotation req

0732bc7

change indents to multiples of 4 spaces for BiocCheck

03fd6bc

don't treat warnings as errors

9823dff

match indentation of LOLA scripts

2d69858

update samples df var for reading genomic regions

f3139b2

fix code style issues, update example config and annotation

b6600a3

update dependencies

024702c

fix dependencies error

fd36c31

runLOLA_iGD.R

1e80b42

add iGD loc into out list

730474e

create multiple iGD input vectors, if userSets > 1, time tests

e999c61

improvements to loadPEP and runLOLA functions

03a99b2

include input class checks, other changes

1ae260d

add missing parenthesis in object class check

72340f6

improve descriptions and other code style issues

1aae8c2

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