Pull request for projection.data combination and cell type selection in panel #1

leprohonmalo · 2020-02-18T08:52:12Z

New function :

panelProjection() : function to project sc_data against reference panel (factorized code from old dataProject).
multiRCApanel() : function that merge projection.data from several call of dataProject
ctQueryReg() : function to select cell type from panel using regular expression, implemented in multiRCApanel, dataProject and panelProjection.
ctQueryTFIDF() : same than previous but using tf-idf metric. Not implemented in other function yet as there is a high variability in result depending on query precision and cut-off score (It still works if you find the good enough one).

Change :

dataProject() : implemented pre-processing for ColonEpiPanel and some small changes to handle problems that may arise from cell type selection.

…theliumPanel

…d of removing them.

…ery using regular expression.

…ction due to cell type selection

…d not implement this function in other functions yet.

leprohonmalo added 11 commits February 11, 2020 09:37

Factorized some code from dataProject.R

7dee9f6

Factorized version of dataProject.R, working on implementing ColonEpi…

7bf4a47

…theliumPanel

Finished to implement ColonEpitheliumPanel in dataProject

0427421

Pre-processing of ColonEpitheliumPanel now combines duplicates instea…

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…d of removing them.

Added ctQueryReg a function to select cell-type (for panel) with a qu…

7a9ed0b

…ery using regular expression.

Corrected function's name in apply line

bd5cfb0

Added cell type selection to panelProjection

1f6d57c

Added cell type selection to dataProject and handling of failed proje…

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…ction due to cell type selection

added multiRCAPanel.R, a function for combination of projection data.

7e2e6de

Added a function to select cell types based on a tf-idf score, but di…

f7db697

…d not implement this function in other functions yet.

Merged dataProject and master, resolved conflict in dataProject.R

c32b759

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