Skip to content
New issue

Have a question about this project? Sign up for a free GitHub account to open an issue and contact its maintainers and the community.

Sign up for GitHub

By clicking “Sign up for GitHub”, you agree to our terms of service and privacy statement. We’ll occasionally send you account related emails.

Already on GitHub? Sign in to your account

docs(getSubnetworkFromIndra): Switch MSstats as dependency, adjust link to groupComparison #22

Merged
merged 2 commits into from
Nov 6, 2024
Merged

docs(getSubnetworkFromIndra): Switch MSstats as dependency, adjust link to groupComparison #22

Show file tree
Hide file tree
Changes from all commits
Commits
Show all changes
2 commits
Select commit Hold shift + click to select a range
05e0277
docs(getSubnetworkFromIndra): Switch MSstats as dependency, add link …
tonywu1999 Nov 6, 2024
aa20704
update manual for visualizeNetworks
tonywu1999 Nov 6, 2024
File filter

Filter by extension

Filter by extension
Conversations
Failed to load comments.
Loading
Jump to
Jump to file
Failed to load files.
Loading
Diff view
Diff view
4 changes: 2 additions & 2 deletions DESCRIPTION
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -20,15 +20,15 @@ Imports:
RCy3,
httr,
jsonlite,
r2r
r2r,
MSstats
Suggests:
data.table,
BiocStyle,
knitr,
rmarkdown,
testthat (>= 3.0.0),
mockery,
MSstats,
MSstatsConvert
VignetteBuilder: knitr
biocViews: ImmunoOncology, MassSpectrometry, Proteomics, Software,
Expand Down
8 changes: 4 additions & 4 deletions R/getSubnetworkFromIndra.R
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -3,14 +3,14 @@
#' Using differential abundance results from MSstats, this function retrieves
#' a subnetwork of protein interactions from INDRA database.
#'
#' @param input output of groupComparison function's comparisionResult table,
#' which contains a list of proteins and their corresponding p-values, logFCs,
#' along with additional HGNC ID and HGNC name columns
#' @param input output of \code{\link[MSstats]{groupComparison}} function's
#' comparisionResult table, which contains a list of proteins and their
#' corresponding p-values, logFCs, along with additional HGNC ID and HGNC
#' name columns
#' @param pvalueCutoff p-value cutoff for filtering. Default is NULL, i.e. no
#' filtering
#'
#' @return list of 2 data.frames, nodes and edges
#' @seealso \code{\link[MSstats]{groupComparison}}
#'
#' @export
#'
Expand Down
10 changes: 4 additions & 6 deletions man/getSubnetworkFromIndra.Rd
View file
Open in desktop

Some generated files are not rendered by default. Learn more about how customized files appear on GitHub.

8 changes: 4 additions & 4 deletions man/visualizeNetworks.Rd
View file
Open in desktop

Some generated files are not rendered by default. Learn more about how customized files appear on GitHub.

Loading