README.md

In WendyLiuLab/BiactivationFlow: What the package does (short line)

To start working with a git checkout:

1. Load the project in RStudio
2. Run roxygen2 over the package by selecting Build -> Document
3. Load the package with devtools::load_all()
4. Run data-raw/preprocess.R
5. Build -> Build and Reload

Summarized data files will be located in inst/extdata.

| Column name | Description | | --- | --- | | FSC.A | Forward scatter AUC | | FSC.H | Forward scatter peak height | | FSC.W | Forward scatter peak width | | SSC.* | Side scatter; as above | | CD86 | Scale value for CD86 staining intensity | | CD206 | Scale value for CD206 staining intensity | | Time | Time to event from acquisition start (s) | | Event.. | Event serial number | | Filename | Filename of original FCS file | | Experiment | Replicate ID | | antibody | "exp" (CD206/CD86) or "iso" (isotype controls) | | m1_concentration | [LPS+IFN-γ] (ng/ml) | | m2_concentration | [IL-4+IL-13] (ng/ml) | | timepoint (if applicable) | Duration of incubation with cytokines (h) |

See the vignettes for examples of normalizing data. Grouping on the antibody column is critical when plotting or summarizing data!

WendyLiuLab/BiactivationFlow documentation built on May 9, 2019, 10:56 p.m.