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Update from adjP to rawP
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sdgamboa committed Sep 12, 2024
1 parent 238805f commit 19b473f
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Showing 3 changed files with 3 additions and 3 deletions.
2 changes: 1 addition & 1 deletion vignettes/articles/HMP_2012_16S_gingival_V35.Rmd
Original file line number Diff line number Diff line change
Expand Up @@ -248,7 +248,7 @@ positives <- createPositives(
object = DA_output,
priorKnowledge = prior_info,
enrichmentCol = "taxon_annotation", namesCol = "new_names",
slot = "pValMat", colName = "adjP", type = "pvalue",
slot = "pValMat", colName = "rawP", type = "pvalue",
# direction = direction,
direction = direction,
threshold_pvalue = 1,
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2 changes: 1 addition & 1 deletion vignettes/articles/HMP_2012_16S_gingival_V35_subset.Rmd
Original file line number Diff line number Diff line change
Expand Up @@ -144,7 +144,7 @@ positives <- createPositives(
object = DA_output,
priorKnowledge = prior_info,
enrichmentCol = "taxon_annotation", namesCol = "new_names",
slot = "pValMat", colName = "adjP", type = "pvalue",
slot = "pValMat", colName = "rawP", type = "pvalue",
direction = direction,
threshold_pvalue = 1,
threshold_logfc = 0,
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2 changes: 1 addition & 1 deletion vignettes/articles/HMP_2012_WMS_gingival.Rmd
Original file line number Diff line number Diff line change
Expand Up @@ -148,7 +148,7 @@ positives <- createPositives(
object = DA_output,
priorKnowledge = prior_info,
enrichmentCol = "taxon_annotation", namesCol = "taxon_name",
slot = "pValMat", colName = "adjP", type = "pvalue",
slot = "pValMat", colName = "rawP", type = "pvalue",
direction = direction,
threshold_pvalue = 1,
threshold_logfc = 0,
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