resolve bioc merge conflicts

nhejazi · Aug 22, 2017 · 9349978 · 9349978
2 parents 4daf357 + 0ac59e9
commit 9349978
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Showing 49 changed files with 13 additions and 3,805 deletions.
diff --git a/.Rbuildignore b/.Rbuildignore
@@ -5,10 +5,8 @@
 ^codecov\.yml$
 ^CONTRIBUTING\.md$
 ^Makefile$
-^\.git$
 ^\.gitignore$
 ^\.gitattributes$
-^data-raw$
 ^paper$
 ^docs$
 ^README\.md$

diff --git a/DESCRIPTION b/DESCRIPTION
@@ -7,16 +7,15 @@ Authors@R: c(
   person("Alan", "Hubbard", email = "hubbard@berkeley.edu", role = "aut"),
   person("Weixin", "Cai", email = "wcai@berkeley.edu", role = "ctb")
   )
-Author: Nima Hejazi [aut, cre, cph]
+Author: Nima Hejazi [aut, cre, cph], Alan Hubbard [aut], Weixin Cai [ctb]
 Maintainer: Nima Hejazi <nhejazi@berkeley.edu>
 Description: This package facilitates the discovery of biomarkers from
   biological sequencing data (e.g., microarrays, RNA-seq) based on the
   associations of potential biomarkers with exposure and outcome variables by
   implementing an estimation procedure that combines a generalization of
   moderated statistics with asymptotically linear statistical parameters
   estimated via targeted minimum loss-based estimation (TMLE).
-Depends:
-  R (>= 3.3)
+Depends: R (>= 3.4)
 License: file LICENSE
 URL: https://github.com/nhejazi/biotmle
 BugReports: https://github.com/nhejazi/biotmle/issues

diff --git a/R/biomarkertmle.R b/R/biomarkertmle.R
@@ -198,3 +198,4 @@ biomarkertmle <- function(se,
   }
   return(biotmle)
 }
+
diff --git a/R/biotmle.R b/R/biotmle.R
@@ -59,3 +59,4 @@ setClassUnion(name = "data.frame_OR_EList", members = c("data.frame", "EList"))
                     topTable = "data.frame"),
        contains = "SummarizedExperiment"
 )
+
diff --git a/R/modtest_ic.R b/R/modtest_ic.R
@@ -40,3 +40,4 @@ modtest_ic <- function(biotmle,
   biotmle@topTable <- as.data.frame(tt)
   return(biotmle)
 }
+
diff --git a/R/plots.R b/R/plots.R
@@ -217,3 +217,4 @@ heatmap_ic <- function(x, ..., design, FDRcutoff = 0.05, top = 25) {
                        ...
                       )
 }
+
diff --git a/docs/LICENSE b/docs/LICENSE
diff --git a/docs/articles/exposureBiomarkers.html b/docs/articles/exposureBiomarkers.html
diff --git a/docs/articles/exposureBiomarkers_files/figure-html/heatmap_limma_results-1.png b/docs/articles/exposureBiomarkers_files/figure-html/heatmap_limma_results-1.png
diff --git a/docs/articles/exposureBiomarkers_files/figure-html/pval_hist_limma_adjp-1.png b/docs/articles/exposureBiomarkers_files/figure-html/pval_hist_limma_adjp-1.png
diff --git a/docs/articles/exposureBiomarkers_files/figure-html/pval_hist_limma_rawp-1.png b/docs/articles/exposureBiomarkers_files/figure-html/pval_hist_limma_rawp-1.png
diff --git a/.../articles/exposureBiomarkers_files/figure-html/volcano_plot_limma_results-1.png b/.../articles/exposureBiomarkers_files/figure-html/volcano_plot_limma_results-1.png
diff --git a/docs/articles/index.html b/docs/articles/index.html
diff --git a/docs/articles/outcomeBiomarkers.html b/docs/articles/outcomeBiomarkers.html