From f2fb8586b7a481d8724605282cf987647b00b9cc Mon Sep 17 00:00:00 2001 From: xushuangbin Date: Tue, 17 Dec 2024 14:38:32 +0800 Subject: [PATCH] adjust the length of some rd lines --- R/methods-fscore.R | 13 ++++++++----- R/methods-sgsa.R | 3 ++- data/datalist | 2 -- man/fscoreDfs.Rd | 13 ++++++++----- man/runSGSA-method.Rd | 3 ++- 5 files changed, 20 insertions(+), 14 deletions(-) diff --git a/R/methods-fscore.R b/R/methods-fscore.R index 7879b65..3c82b89 100644 --- a/R/methods-fscore.R +++ b/R/methods-fscore.R @@ -90,12 +90,15 @@ #' colnames(sce2) <- colnames(svpe) #' #' # Mocking up some relationship score between new feature and gene -#' fscore1 <- lapply(seq(nrow(sce1)), function(i) abs(rnorm(5, 0.5)) |> setNames(sample(rownames(svpe),5))) |> -#' List() |> -#' DataFrame() |> setNames("rwr_score") +#' fscore1 <- lapply(seq(nrow(sce1)), function(i) abs(rnorm(5, 0.5)) |> +#' setNames(sample(rownames(svpe),5))) |> +#' List() |> +#' DataFrame() |> setNames("rwr_score") #' rownames(fscore1) <- rownames(sce1) -#' fscore2 <- lapply(seq(nrow(sce2)), function(i) abs(rnorm(5, 0.8)) |> setNames(sample(rownames(svpe),5))) |> -#' List() |> DataFrame() |> setNames("hyper_test") +#' fscore2 <- lapply(seq(nrow(sce2)), function(i) abs(rnorm(5, 0.8)) |> +#' setNames(sample(rownames(svpe),5))) |> +#' List() |> +#' DataFrame() |> setNames("hyper_test") #' # Setting the score #' fscoreDfs(sce1) <- list() #' fscoreDfs(sce2) <- list() diff --git a/R/methods-sgsa.R b/R/methods-sgsa.R index 06276d5..a978452 100644 --- a/R/methods-sgsa.R +++ b/R/methods-sgsa.R @@ -107,7 +107,8 @@ #' # #' # supporting the list with names or gson object or the gmt file #' # online gmt file is also be supported -#' # such as https://data.broadinstitute.org/gsea-msigdb/msigdb/release/2023.2.Hs/c2.cp.biocarta.v2023.2.Hs.symbols.gmt +#' # such as +#' # https://data.broadinstitute.org/gsea-msigdb/msigdb/release/2023.2.Hs/h.all.v2023.2.Hs.symbols.gmt #' #' data(CellCycle.Hs) #' sceSubPbmc <- runSGSA(sceSubPbmc, gset.idx.list = CellCycle.Hs, gsvaExp.name = 'CellCycle') diff --git a/data/datalist b/data/datalist index 5134435..721959b 100644 --- a/data/datalist +++ b/data/datalist @@ -4,5 +4,3 @@ SenMayoSymbol sceSubPbmc CellCycle.Hs hpda_spe_cell_dec -pdac_a_sce -pdac_a_spe diff --git a/man/fscoreDfs.Rd b/man/fscoreDfs.Rd index 13ac843..7da6861 100644 --- a/man/fscoreDfs.Rd +++ b/man/fscoreDfs.Rd @@ -103,12 +103,15 @@ rownames(sce2) <- paste0("KEGG:", seq(nrow(sce2))) colnames(sce2) <- colnames(svpe) # Mocking up some relationship score between new feature and gene -fscore1 <- lapply(seq(nrow(sce1)), function(i) abs(rnorm(5, 0.5)) |> setNames(sample(rownames(svpe),5))) |> - List() |> - DataFrame() |> setNames("rwr_score") +fscore1 <- lapply(seq(nrow(sce1)), function(i) abs(rnorm(5, 0.5)) |> + setNames(sample(rownames(svpe),5))) |> + List() |> + DataFrame() |> setNames("rwr_score") rownames(fscore1) <- rownames(sce1) -fscore2 <- lapply(seq(nrow(sce2)), function(i) abs(rnorm(5, 0.8)) |> setNames(sample(rownames(svpe),5))) |> - List() |> DataFrame() |> setNames("hyper_test") +fscore2 <- lapply(seq(nrow(sce2)), function(i) abs(rnorm(5, 0.8)) |> + setNames(sample(rownames(svpe),5))) |> + List() |> + DataFrame() |> setNames("hyper_test") # Setting the score fscoreDfs(sce1) <- list() fscoreDfs(sce2) <- list() diff --git a/man/runSGSA-method.Rd b/man/runSGSA-method.Rd index add1781..deaa37d 100644 --- a/man/runSGSA-method.Rd +++ b/man/runSGSA-method.Rd @@ -185,7 +185,8 @@ sceSubPbmc <- runMCA(sceSubPbmc, assay.type = 'logcounts') # # supporting the list with names or gson object or the gmt file # online gmt file is also be supported -# such as https://data.broadinstitute.org/gsea-msigdb/msigdb/release/2023.2.Hs/c2.cp.biocarta.v2023.2.Hs.symbols.gmt +# such as +# https://data.broadinstitute.org/gsea-msigdb/msigdb/release/2023.2.Hs/h.all.v2023.2.Hs.symbols.gmt data(CellCycle.Hs) sceSubPbmc <- runSGSA(sceSubPbmc, gset.idx.list = CellCycle.Hs, gsvaExp.name = 'CellCycle')