Njjacobs

.gitignore

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 /.quarto/
+
+**/*.quarto_ipynb

course/01_InstallingRPackages/homeworks/README.md

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+
 # Turning In Optional Take-Home Problems
 
 This folder is for the use of submitting your completed Take-Home Problems for evaluation by course instructors. Please see [Getting Help](/course/00_Homeworks/index.qmd) walkthrough for more detailed instructions. 
 
-Within your branch, inside this "homeworks" folder, create a new folder (name it with your GitHub username). Then copy all files you will be submitting within your folder.  Then commit the change to git, and push to GitHub. See [Getting Help](/course/00_Homeworks/index.qmd)for details on submitting the pull request to the UMGCCCFCSR/CytometryInR homework branch. 
+Within your branch, inside this "homeworks" folder, create a new folder (name it with your GitHub username). Then copy all files you will be submitting within your folder.  Then commit the change to git, and push to GitHub. See [Getting Help](/course/00_Homeworks/index.qmd)for details on submitting the pull request to the UMGCCCFCSR/CytometryInR homework branch. 
+
+Is this where you said we can "email" you? 

course/01_InstallingRPackages/homeworks/njjacobs/Week 1.qmd

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+---
+title: "Week 1 Homework NJ"
+format: html 
+Author: "Natalie Jacobs" 
+---
+
+
+# Problem 1
+We installed PeacoQC during this session, but we didn’t have time to explore what functions are present within the package. Using what you have learned about accessing documentation, figure out and list what functions it contains
+
+# Answer 1
+
+```{r}
+library(PeacoQC)
+ls("package:PeacoQC")
+```
+
+# output 
+[1] "PeacoQC" "PeacoQCHeatmap" "PlotPeacoQC" "RemoveDoublets" "RemoveMargins" 
+
+# Problem 2
+
+Take a closer look at the list of Bioconductor cytometry packages. Report back on how many there are currently in Bioconductor, the author/maintainer with the most contributed cytometry R packages, and a couple packages that you would be interested in exploring more in-depth later in the course.
+
+# Answer 2
+
+There are over 2,361 packages listed on Bioconductor.org. 
+
+Hervé Pagès maintains a lot of highly ranked packages, so does Guangchuang Yu, and Aaron Lun
+
+TENxPBMCData, SamSPECTRAL, cytofWorkflow, RNAseq123, rnaseqGene, GEOMxWorkflows packages looks interesting 
+
+# Problem 3
+There is another way to install R packages, using the newer pak package. Positron uses this when installing suggested dependencies. After learning more about it via the documentation and it’s pkgdown website, I would like you to attempt to install the following three R packages using this newer method: “broom”, “cytoMEM”, “DillonHammill/CytoExploreR”.
+Take screenshots, and in a new quarto markdown document, describe how the installation process differed from what you saw for install.packages(), install() and install_github().
+
+# Answer 3 
+
+Broom and cytoMEM installed easily without having to know if from CRAN or Bioconductor. I wasn’t able to install DillonHammill/CytoExploreR with pak method because of an error with package dependencies. I tried install.packages but the package was not available for this version of R. 

course/02_FilePaths/homeworks/njjacobs/README.md

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+# Week-2
+

course/02_FilePaths/homeworks/njjacobs/filepaths copy.qmd

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+---
+Title: Homework Week 2 
+FileType: HTML
+Author: Natalie Jacobs 
+---
+# Week 2 Homework  
+
+# Problem 1 
+Plug in an external hard-drive or USB into your computer. Manually, create a folder within called “TargetFolder”. Try to programmatically specify the file path to identify the folders and files present on your external drive. Then, try to copy your .fcs files from their current folder on your desktop to the TargetFolder on your drive using R. Remember, just copy, no deletion, you need to walk before you can run :D
+
+# Answer 1  
+See screenshot of copied files in images folder 
+```{r}
+dir.exists("E:/")
+list.files("E:/", all.files = TRUE)                           
+```
+part 2 
+```{r}
+TargetPath <- "E:/TargetFolder"
+dir.exists(TargetPath)
+getwd()
+desktopPath <-"y:/documents/Week-2"
+fcs_folder <- file.path(desktopPath, "data")
+list.files(fcs_folder)
+fcs_files <- list.files(desktopPath, pattern = "\\.fcs$", full.names = TRUE, recursive = TRUE, ignore.case = TRUE)
+fcs_files
+length(fcs_files)
+list.dirs("E:/", recursive = FALSE)
+target_path <- file.path("E:/", "TargetFolder")
+dir.exists(target_path)
+file.copy(from = fcs_files, to = target_path)
+```
+I don't know why preview is showing FALSE  after file.copy(from = fcs_files, to = target_path) when it is showing TRUE on the console and the files successfully copied to the USB 
+# Problem 2
+ In this session, we used list.files() with the “full.names argument” set to TRUE, as well as the basename() function to identify specific files. But what if you wanted a particular directory. Run list.files() with “full.names argument” and “recursive” argument set to TRUE, and then search online to find an R function that would retrieve the “” individual directory folders.
+
+# Answer 2
+
+```{r}
+files <- list.files(path = ".",full.names = TRUE,recursive = TRUE)
+unique(dirname(files))
+```
+or
+
+```{r}
+list.dirs()
+```
+# Problem 3
+ R packages often come with internal datasets, that are typically used for use in the help documentation examples. These can be accessed through the use of the system.file() function. See an example below.
+
+system.file("extdata", package = "FlowSOM")
+
+Using what we have learned about file.path navigation, search your way down the file.directory of the FlowSOM and flowWorkspace packages, and identify any .fcs files that are present for use in the documentation.
+
+# Answer 3 
+For FlowSOM 
+```{r}
+flowSOM_path <- system.file(package = "FlowSOM")
+
+flowSOM_files <- list.files(flowSOM_path,
+                            pattern = "\\.fcs$",
+                            full.names = TRUE,
+                            recursive = TRUE,
+                            ignore.case = TRUE)
+
+flowSOM_files
+
+```
+For flowWorkspace
+
+```{r}
+flowWorkspace_path <- system.file(package = "flowWorkspace")
+
+flowWorkspace_files <- list.files(flowWorkspace_path,
+                                   pattern = "\\.fcs$",
+                                   full.names = TRUE,
+                                   recursive = TRUE,
+                                   ignore.case = TRUE)
+
+flowWorkspace_files
+
+```
+Returned 0 .fcs files. Have to go to companion package like flowWorkpaceData for eample datasets 
+Hardcoding way for my own reference
+```{r}
+system.file(".",package = "FlowSOM")
+CheckFiles <- "C:/Users/njjacobs/AppData/Local/Programs/R/R-4.5.2/library/FlowSOM/."
+system.file("extdata", package = "FlowSOM")
+files <- "C:/Users/njjacobs/AppData/Local/Programs/R/R-4.5.2/library/FlowSOM/extdata"
+list.files(files) 
+```
+There is a .fcs file in the FlowSOM extdata folder called 68983.fcs