| Title: | What the Package Does (Title Case) |
|---|---|
| Description: | More about what it does (maybe more than one line) Use four spaces when indenting paragraphs within the Description. |
| Authors: | Rainer M. Krug [aut, cre], SNF Project 310030_188431 [fnd] |
| Maintainer: | Rainer M. Krug <[email protected]> |
| License: | MIT + file LICENSE |
| Version: | 0.8.13 |
| Built: | 2024-11-19 06:12:14 UTC |
| Source: | https://github.com/LEEF-UZH/LEEF.measurement.flowcytometer |
Check if data in input folder is OK and move to raw data folder
add_new_data(input, output)add_new_data(input, output)
input |
The folder, where a folder |
output |
A folder, which contains a subfolder called |
a list which contains the individual reseults for each file.
TRUE if moved, FALSE if an error occured. Details of the eror
re in the error files in the input/flowcytometer directory.
This function is extracting data to be added to the database (and therefore make accessible for further analysis and forecasting)
from .fcs files.
extractor_flowcytometer(input, output)extractor_flowcytometer(input, output)
input |
directory from which to read the data |
output |
directory to which to write the data |
invisibly TRUE when completed successful
This function is extracting data to be added to the database
(and therefore make accessible for further analysis and forecasting)
from .fcs files.
extractor_flowcytometer_gating(input, output)extractor_flowcytometer_gating(input, output)
input |
directory from which to read the data |
output |
directory to which to write the data |
invisibly TRUE when completed successful
This function is extracting data to be added to the database
(and therefore make accessible for further analysis and forecasting)
from .fcs files.
extractor_flowcytometer_preparation(input, output)extractor_flowcytometer_preparation(input, output)
input |
directory from which to read the data |
output |
directory to which to write the data |
invisibly TRUE when completed successful
file
Load parameter from file
load_parameter(file = "parameter.yaml")load_parameter(file = "parameter.yaml")
file |
name of parameter file |
invisibly TRUE
assign the function to a new cvariable and the name of the function woll be used for the parameter name. e.g:
fps <- par_template
par_template(value)par_template(value)
value |
if missing, the value of the parameter will be returned, |
the (new) value of the argument
Just copy all files
pre_processor_flowcytometer(input, output)pre_processor_flowcytometer(input, output)
input |
directory from which to read the data |
output |
directory to which to write the data |
invisibly TRUE when completed successful
Convert all .c6 files in flowcytometrie folder to .fcs files in output folder
pre_processor_flowcytometer_c6(input, output)pre_processor_flowcytometer_c6(input, output)
input |
directory from which to read the data |
output |
directory to which to write the data |
invisibly TRUE when completed successful
Print the flowcytometer parameter
print_parameter(print_as_yaml = TRUE, echo = TRUE)print_parameter(print_as_yaml = TRUE, echo = TRUE)
print_as_yaml |
Print in yaml formated text; |
echo |
if |
invisible returns list of parameter for further processing
Check if data in raw data folder is OK
raw_data_ok(input)raw_data_ok(input)
input |
raw data folder containing flowcytometer data, i.e usually is |
TRUE if ok, FALSE or list of problems if not
## Not run: raw_data_ok() ## End(Not run)## Not run: raw_data_ok() ## End(Not run)
Register the processing of flowcytometer data in the LEEF package
register()register()
invisibly TRUE when completed successful
.yaml fileSave parameter into .yaml file
save_parameter(file = "parameter.yaml")save_parameter(file = "parameter.yaml")
file |
name of parameter file |
invisibly TRUE