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Add option to use anndataR to read in tables #62

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merged 3 commits into from
Nov 13, 2024
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LouiseDck
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Current usage:
Install anndataR as such:
devtools::install_github("keller-mark/anndataR", ref = "spatialdata")

Changes:

in file read.R

  • add readTable_anndataR function that uses anndataR to read & convert to SingleCellExperiment
  • rename readTable to readTable_basilisk
  • add readTable function that disambiguates between the two functions based on a parameter passed by readSpatialData

in file test_methods.R

  • add test that reads using anndata & basilisk & zellkonverter and one that uses anndataR, check for differences

@LouiseDck LouiseDck marked this pull request as ready for review November 12, 2024 15:36
@LouiseDck
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I think this should probably only be merged here when this PR in anndataR is merged.

@HelenaLC HelenaLC merged commit 3f96da7 into HelenaLC:main Nov 13, 2024
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