Loading and transforming the data to create a flow cytometry dataset from FCS files for the analysis with the cyCONDOR workflow.
Usage
prep_fcd(
data_path,
max_cell,
useCSV = FALSE,
transformation = NULL,
remove_param = NULL,
anno_table,
filename_col,
seed = 91,
separator_anno = ",",
separator_fc_csv = ",",
simple_names = TRUE,
truncate_max_range = FALSE,
emptyValue = TRUE,
ignore.text.offset = FALSE,
verbose = FALSE,
cross_path_with_anno = FALSE,
cofactor = 5
)Arguments
- data_path
Folder where the .fcs files or .csv files are stored.
- max_cell
Number of cells to use for each file (set to a high number if you want to use all available events).
- useCSV
Flag if the input are .csv files and not .fcs (experimental).
- transformation
Transformation to perform. Select one of the following:
"auto_logi"(autologicle, recommended for flow cytometry data),"arcsinh"(arcsinh transformation with cofactor 5),"clr"(centered-log-ratio) or"none"(no transformation).- remove_param
Parameters to be removed from the
fcd, "inTime" should be kept.- anno_table
Path to the annotation table text file. The annotation table should contain one column with the file names of all .fcs or .csv files to read in and optionally additional columns with further sample information (e.g. "sample_id", "condition").
- filename_col
Name of the column of the
anno_tablecontaining the file name matching with the .fcs/.csv files.- seed
A seed is set for reproducibility.
- separator_anno
Separator used in the annotation file, by default
separator_anno = ",".- separator_fc_csv
Separator used in the cytometry data .csv files, by default
separator_anno = ",".- simple_names
If TRUE only the channel description is used to name the column, if FALSE both channel name and description are pasted together.
- truncate_max_range
From FlowCore: logical type. Default is FALSE. can be optionally turned off to avoid truncating the extreme positive value to the instrument measurement range .i.e.'$PnR'.
- emptyValue
From FlowCore: boolean indicating whether or not we allow empty value for keyword values in TEXT segment. It affects how the double delimiters are treated. IF TRUE, The double delimiters are parsed as a pair of start and end single delimiter for an empty value. Otherwise, double delimiters are parsed one part of string as the keyword value. default is TRUE.
- ignore.text.offset
From FlowCore: whether to ignore the keyword values in TEXT segment when they don't agree with the HEADER. Default is FALSE, which throws the error when such discrepancy is found. User can turn it on to ignore TEXT segment when he is sure of the accuracy of HEADER so that the file still can be read.
- verbose
Default FALSE, if TRUE the at each file loaded something is printed in the screen.
- cross_path_with_anno
Defautl FALSE. If TRUE is the 'data_path' contains more files then the annotation table only the overlap will be loaded.
- cofactor
cofactor used for 'arcsinh' transformation, default 5, can be set to 150 for HDFC data.