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Bioconductor Warnings #159

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merged 19 commits into from
Apr 16, 2024
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9a13be8
fix: error with summarizeSensitivity Profiles on LongTables where it …
jjjermiah Feb 7, 2024
3d54535
add column arguments to drugDoseResponseCurve
jjjermiah Feb 8, 2024
650d0e5
Update cellline parameter in drugDoseResponseCurve function
jjjermiah Feb 21, 2024
ed19577
docs: add documentation for summarizeSensitivityProfiles
jjjermiah Mar 1, 2024
4e38299
fix: Refactor buildComboProfiles function in computeSynergy.R example…
jjjermiah Apr 8, 2024
a7d8565
fix: Add sample_col and treatment_col arguments to drugDoseResponseCu…
jjjermiah Apr 8, 2024
5e17a0c
fix: remove unlinked [boolean] term as it causes warnings
jjjermiah Apr 8, 2024
c197d9d
chore: delete CreatingPharmacoSet.R Remove CreatingPharmacoSet.R vign…
jjjermiah Apr 8, 2024
7361b1e
fix: Update CreatingPharmacoSet.Rmd to install required packages if n…
jjjermiah Apr 8, 2024
f9eb62e
docs: update Vignette to reflect new changes
jjjermiah Apr 8, 2024
048e913
chore: .Rbuildignore and DESCRIPTION Update .Rbuildignore and DESCRIP…
jjjermiah Apr 8, 2024
f5ae5e1
update CreatingPharmacoSet.Rmd Refactor vignette code to install requ…
jjjermiah Apr 8, 2024
c52e6c6
Update version to 3.7.5 in DESCRIPTION file
jjjermiah Apr 12, 2024
b71fff2
docs: update all docs with roxygen.
jjjermiah Apr 12, 2024
032e864
refactor: Refactor code in R/methods-[.R, R/updateObject-methods.R, s…
jjjermiah Apr 12, 2024
592a42e
ci: update R-CMD-check-bioc.yml Update branch filter in R-CMD-check-b…
jjjermiah Apr 12, 2024
9324b7d
Update branch filter in R-CMD-check-bioc.yml workflow
jjjermiah Apr 12, 2024
4a80e0b
Update branch filter in R-CMD-check-bioc.yml workflow
jjjermiah Apr 12, 2024
c4967cc
Merge pull request #158 from bhklab/156-warning-on-bioc
jjjermiah Apr 12, 2024
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fix: remove unlinked [boolean] term as it causes warnings
jjjermiah committed Apr 8, 2024
commit 5e17a0ca1bc81e12eb9c6a9e313bb82f071eaa9c
4 changes: 2 additions & 2 deletions R/methods-summarizeSensitivityProfiles.R
Original file line number Diff line number Diff line change
@@ -18,8 +18,8 @@
#' @param sample_col [character] The name of the column in the profiles assay that contains the sample IDs.
#' @param drugs [character] The drugs to be summarized. If any drugs have no data, they will be filled with missing values.
#' @param summary.stat [character] The summary method to use if there are repeated cell line-drug experiments. Choices are "mean", "median", "first", "last", "max", or "min".
#' @param fill.missing [boolean] Should the missing cell lines not in the molecular data object be filled in with missing values?
#' @param verbose [boolean] Should the function print progress messages?
#' @param fill.missing Should the missing cell lines not in the molecular data object be filled in with missing values?
#' @param verbose Should the function print progress messages?
#'
#' @return [matrix] A matrix with cell lines going down the rows, drugs across the columns, with the selected sensitivity statistic for each pair.
#'