TODO.md

In ndhutso/geneSummary: Summarize GEOquery data

[x] create base working package based on a main [x] use Biobase to smooth out data table formation (going to break a lot of stuff in analyze used for graphs) [x] Tidy up functions [ ] refactor functions to be more general [x] ask if all geo data is in same format to implement already written functions [x] split up analysis and visualize into separate functions to prep data and graph/tabularize in different ways [x] update extraction functions to take a list of BioConductor formatted data, combine them, and look for a specific data set or extract a variable from the combined data [ ] implement generalized graphing (take filtered table, and if less than 10 rows, create different plots) [x] change any $Symbol variable to grep search of column names because some data sets use gene symbol instead of just symbol [ ] create shiny interface to search, tabularize, and graph different sets of data [x] change the amount of inputs based on the type of data table selected [x] create different titles for different types of data tables [x] implement pre-defined graphs (change box to ggplot) [x] give user ability to save data [x] find way to include row names [x] give user ability to choose pages of a data set with multiple data frames [x] improved moving through multiple data sets [x] pass names of data sets back when returning a list [x] use selectInput to choose which data set and what type of data set to save [x] add search by sample ID [x] allow user to choose which variable they want to search by instead of just geneSymbol, potentially allow addition of more filters [x] limit amount of filters based off number of columns [x] take away filters when type of data table is changed [x] pass choices to selectize (maybe just text input) [x] fix reset of selection [x] fix save function [x] remove debug numbering [x] only use inputs that exist for filtering [x] make it so that geneExpression tables only have 2 options for filters [x] implement numeric filters [ ] make an option for a filter disappear from the list for additional filters/make identical filter by's compatible [x] FIX variable "len" INITIALIZATION [ ] look at DT table filters [x] give checkbox option for long format of data which is easier for graphing [x] add ID column to extExp or move gene symbols to rownames [x] fix extraction functions to work with lists with multiple data sets as input [x] change if statements and output because some inputs cant have all their data sets combined [x] clean up column names for extExp (necessary to fix extExp function) [x] fix symbol column [x] check if other functions need a similar update [x] test extGene and extSample for multiple data sets [x] implement recount2 data [x] figure out how pass a text input to get rse objects [x] create new function to extract gene expression for RSE data [x] apply filters [x] make sure long style format works [x] update save function [x] fix runShiny [ ] DOCUMENTATION [ ] fix issue where GEOquery, stringr aren't importing - make biobase and them required

ndhutso/geneSummary documentation built on Nov. 4, 2019, 8:43 p.m.