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iGD integration#37

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joseverdezoto wants to merge 29 commits intonsheff:masternsheff/LOLA:masterfrom joseverdezoto:dev_igdjoseverdezoto/LOLA:dev_igdCopy head branch name to clipboard

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Commits on Oct 21, 2019

• function to create a list from a PEP object

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  7ef39b7

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• add code to load data as GRanges list

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Commits on Oct 22, 2019

• use readBED instead of fread

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• take out ellipses in file path

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Commits on Oct 23, 2019

• update description

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  ca44994

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• Delete readPEP.R

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• add names to list elements

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

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Commits on Oct 24, 2019

• preliminary annotation and config file for ucsc example

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• add export and example

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Commits on Oct 28, 2019

• add caching capability to loadPEPdb

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Commits on Oct 29, 2019

• store cached regions next to annotation and config files

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Commits on Nov 25, 2019

• fix simpleCache message

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  321b508

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Commits on Dec 4, 2019

• delete old version of the loadPEPdb function

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Commits on Dec 13, 2019

• change columns names to meet LOLA annotation req

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Commits on Jan 21, 2020

• change indents to multiples of 4 spaces for BiocCheck

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Commits on Feb 19, 2020

• don't treat warnings as errors

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Commits on Feb 20, 2020

• match indentation of LOLA scripts

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• update samples df var for reading genomic regions

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Commits on Feb 21, 2020

• fix code style issues, update example config and annotation

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  b6600a3

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• update dependencies

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• fix dependencies error

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Commits on Mar 13, 2020

• runLOLA_iGD.R

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Commits on Mar 16, 2020

• add iGD loc into out list

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

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Commits on Mar 27, 2020

• improvements to loadPEP and runLOLA functions

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Commits on Mar 30, 2020

• include input class checks, other changes

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  1ae260d

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• add missing parenthesis in object class check

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  72340f6

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• improve descriptions and other code style issues

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