Description Usage Arguments Details Value Examples
View source: R/PrepareGatingSetList4Compass.R
This function accepts GatingSets and/or reads in multiple FlowJo workspace xml files and their associated FCS files. It then combines them all into a single GatingSetList, extracting the user-provided keywords and checking that the batches are combine-able along the way. GatingSets should already have keywords. The final GatingSetList is saved to a user-provided output directory by default. You can then use it directly with COMPASS or modify it further.
1 2 3 4 5 |
xmlFiles |
character vector (xmlFiles AND/OR gsDirs AND/OR gsList is required) |
fcsFiles |
(Optional) character vector. Only needed if fcs and xml files exist in different directories. |
gsDirs |
character vector (xmlFiles AND/OR gsDirs AND/OR gsList is required) |
gsList |
list of GatingSet objects (xmlFiles AND/OR gsDirs AND/OR gsList is required) |
outDir |
directory in which to save the final GatingSetList |
sampleGroups |
(Optional) numeric vector. Specify this if the flowJo sample group is not 3 for all batches. |
keywords2import |
(Optional) character vector. List of keywords to import from FlowJo workspace and into pData. |
keyword4samples2exclude |
(Optional) keyword used to identify samples for exclusion |
samples2exclude |
(Optional) character vector. When making GatingSetList, excludes samples whose keyword4samples2exclude column matches patterns in this vector (using 'grepl'). |
returnGSList |
(Optional) Return the GatingSetList instead of saving it. Default FALSE |
Note 1: All the batches need to have the same gating tree, so this function will drop unshared nodes and channels from the batches to be merged. TODO: make option to turn off default Note 2: Marker names and channel names must all be the same across the batches.
Nothing, or GatingSetList if requested
1 2 3 4 5 6 7 8 9 10 11 12 | ## Not run:
prepare.gating.set.list.4.compass(xmlFiles=c("/home/Batch1Files/Batch1FlowJoWorkspace.xml",
"/home/Batch2Files/Batch2FlowJoWorkspace.xml",
"/home/Batch3Files/Batch3FlowJoWorkspace.xml",
"/home/Batch4Files/Batch4FlowJoWorkspace.xml"),
outDir="/home/GatingSetListOutDir",
keywords2import=c("Barcode", "Antigen", "PATIENT ID"),
keyword4samples2exclude="Barcode",
samples2exclude=c('1234567890', '1234567891', '1234567892', '1234567893', '1234567894'))
## End(Not run)
TODO: Write tests. - When keyword4samples2exclude and gsList and/or gsDirs are provided. - When keyword4samples2exclude and xmlFiles are provided
|
Add the following code to your website.
For more information on customizing the embed code, read Embedding Snippets.