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Update analyses/cell-type-wilms-tumor-06/scripts/06b_build-normal_ref…
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…erence.R

Co-authored-by: Stephanie Spielman <[email protected]>
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@maud-p @sjspielman
maud-p and sjspielman authored Oct 29, 2024
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3 changes: 3 additions & 0 deletions analyses/cell-type-wilms-tumor-06/scripts/06b_build-normal_reference.R
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Expand Up @@ -4,6 +4,9 @@ repository_base <- rprojroot::find_root(rprojroot::is_git_root)
# The path to this module
module_base <- file.path(repository_base, "analyses", "cell-type-wilms-tumor-06")

# Define threshold score. Only cells with annotations greater than this threshold will be used
score_threshold <- 0.85

# Select samples that haven't be pre-treated with chemotherapies
# Even if normal cells shouldn't be affected by chemotherapy in terns of CNV, we decided to only take endothelial and immune cells from non-treated samples to build the reference of normal cells

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