prepare_data | R Documentation |
This is a wrapper function that takes you from a directory of .fcs files or a flowset to a transformed tibble.
prepare_data(
data_dir = NULL,
flowset = NULL,
markers = NULL,
pattern = "\\.fcs",
metadata = NULL,
filename_col = "filename",
sample_ids = NULL,
batch_ids = NULL,
condition = NULL,
anchor = NULL,
down_sample = TRUE,
sample_size = 5e+05,
sampling_type = "random",
seed = 473,
panel = NULL,
panel_channel = "fcs_colname",
panel_antigen = "antigen",
transform = TRUE,
cofactor = 5,
derand = TRUE,
.keep = FALSE,
clean_colnames = TRUE
)
data_dir |
Directory containing the .fcs files |
flowset |
Optional: Prepare a flowset instead of a directory of fcs files |
markers |
The markers to transform on |
pattern |
The pattern to use to find the files in the folder |
metadata |
Optional: Can be either a filename or data.frame of the metadata file. Please give the full path from working directory to metadata file |
filename_col |
Optional: The column in the metadata containing the fcs filenames. Needed if metadata is given, but sample_ids is not |
sample_ids |
Optional: If a character, it should be the sample column in the metadata. If its a vector, it should have the same length as the total flowset. If NULL, sample ids will be the file names. If a single value, all rows will be assigned this value. |
batch_ids |
Optional: If a character, it should be the column in the metadata containing the batch ids. If its a vector, it should have the same length as the total flowset. If a single value, all rows will be assigned this value. |
condition |
Optional: The column in the metadata containing the condition. Will be used as the covariate in ComBat, but can be specified later. You may use this to add a different column of choice, in case you want to use a custom column in the ComBat model matrix. |
anchor |
Experimental: The column in the metadata referencing the anchor samples (control references). Will be used as a covariate in ComBat, if specified. Please be aware that this column may be confounded with the condition column. You may use this to add a different column of choice, in case you want to use a custom column in the ComBat model matrix. You may use a custom column name, but it is good practice to add the name to the 'non_markers' object exported by cyCombine, to reduce the risk of unexpected errors. |
down_sample |
If TRUE, the output will be down-sampled to size sample_size |
sample_size |
The size to down-sample to. If a non-random sampling type is used and a group contains fewer cells than the sample_size, all cells of that group will be used. |
sampling_type |
The type of down-sampling to use. "random" to randomly select cells across the entire dataset, "batch_ids" to sample evenly (sample_size) from each batch, or "sample_ids" sample evenly (sample_size) from each sample. |
seed |
The seed to use for down-sampling |
panel |
Optional: Panel as a filename or data.frame. Is used to define colnames from the panel_antigen column |
panel_channel |
Optional: Only used if panel is given. It is the column name in the panel data.frame that contains the channel names |
panel_antigen |
Optional: Only used if panel is given. It is the column name in the panel data.frame that contains the antigen names |
transform |
If TRUE, the data will be transformed; if FALSE, it will not. |
cofactor |
The cofactor to use when transforming |
derand |
Derandomize. Should be TRUE for CyTOF data, otherwise FALSE. |
.keep |
Keep all channels. If FALSE, channels that are not transformed are removed |
clean_colnames |
(Default: TRUE). A logical defining whether column names should be cleaned or not. Cleaning involves removing isotope tags, spaces, dashes, underscores, and all bracket types. |
Other dataprep:
compile_fcs()
,
convert_flowset()
,
transform_asinh()
## Not run:
uncorrected <- data_dir %>%
prepare_data(metadata = "metadata.csv",
markers = markers,
filename_col = "FCS_name",
batch_ids = "Batch",
condition = "condition",
down_sample = FALSE)
## End(Not run)
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