update readme

README.md

@@ -148,16 +148,16 @@ At the end of this process, the directory `$AF_SAMPLE_DIR/quants/pbmc1k_v3/quant
 **R** : In [R](https://www.r-project.org/), you can make use of the `R` [`load_fry()`](https://github.com/COMBINE-lab/usefulaf/blob/main/R/load_fry.R) function here, and read the input with the command:
 
 ```{R}
-m <- load_fry("$AF_SAMPLE_DIR/quants/pbmc1k_v3/quant", which_counts=c('S', 'A'))
+m <- load_fry("$AF_SAMPLE_DIR/quants/pbmc1k_v3/quant")
 ```
 
-where `$AF_SAMPLE_DIR` is appropriately replaced by the path to the working directory we chose at the start of this exercise.  This will return a [SingleCellExperiment](https://bioconductor.org/packages/release/bioc/html/SingleCellExperiment.html) object containing the counts for this experiment.  The stand-alone `load_fry()` function has been merged into the [`fishpond`](https://bioconductor.org/packages/release/bioc/html/fishpond.html) package and will be part of the next release.
+where `$AF_SAMPLE_DIR` is appropriately replaced by the path to the working directory we chose at the start of this exercise.  This will return a [SingleCellExperiment](https://bioconductor.org/packages/release/bioc/html/SingleCellExperiment.html) object containing the counts for this experiment.  The stand-alone `load_fry()` function is part of [`fishpond`](https://bioconductor.org/packages/release/bioc/html/fishpond.html), and the function is documented in detail [here](https://mikelove.github.io/fishpond/reference/loadFry.html).
 
 
 **Python** : In [python](https://www.python.org/), you can make use of the `python` [`load_fry()`](https://github.com/COMBINE-lab/usefulaf/blob/main/python/load_fry.py) function, which relies on [scanpy](https://scanpy.readthedocs.io/en/stable/).  To read the input you can use the following command:
 
 ```{python}
-m = load_fry("$AF_SAMPLE_DIR/quants/pbmc1k_v3/quant", which_counts=['S','A'])
+m = load_fry("$AF_SAMPLE_DIR/quants/pbmc1k_v3/quant")
 ```
 
 where, again `$AF_SAMPLE_DIR` is appropriately replaced by the path to the working directory we chose at the start of this exercise.  This will return a `scanpy` [`AnnData`](https://anndata.readthedocs.io/en/latest/) object with the counts.