WHY marker symbols, not channel names: detector/channel names are
instrument-specific and alter.names = TRUE mangles them (e.g. [[RB613]]-A
becomes X..RB613...A). The biological identity lives in $PnS, which on this
instrument reads "CD45 : SparkUV-387 - Area" – the symbol is the text before
" : ". Building an embedding on channel names (as the original template did)
means no marker identity ever reaches the analysis.
Usage
read_fcs_resolved(
path,
sample_id = NULL,
max_events = 0L,
ignore_channels = NULL,
margins = c("remove", "cap")
)Arguments
- path
File path.
- sample_id
The sample id.
- max_events
The max events. Default
0L.- ignore_channels
Character vector of marker names to drop before the panel fingerprint is taken, or NULL. Names match whole and case-insensitively; a name containing
*is treated as a glob.- margins
"remove"(default) drops every event at the top of the range of a marker or scatter channel;"cap"keeps the event and sets the value to the top of the range instead, which is what earlier versions did.
Value
list(exprs, marker_cols, scatter_cols, channel_names, descs, keywords, channel_range, margin, n_events, n_events_file, subsampled, file, sample_id)
Details
Note: FCS files larger than 99,999,999 bytes cannot express their data offset in the 8-character HEADER field and write 0 there; the true offsets live in the $BEGINDATA/$ENDDATA keywords. flowCore handles this fallback internally.
LOG-AMPLIFIED DATA ARE LINEARISED. An analog instrument with log amplifiers
writes integer channel numbers on a log scale and says so in $PnE. Every
transform this package applies assumes linear intensities, so those channels
are converted first, exactly as flowCore's own default does: see
linearise_channels().
MARGIN EVENTS ARE REMOVED. An event at or beyond the top of a channel's
range has no true value in that channel, so it is dropped, as flowAI and
PeacoQC's RemoveMargins() do. See margin_events() for which channels are
judged, and margins = "cap" for the earlier behaviour.