keyword-methods.RdAccessor and replacement methods for items in the description slot (usually
read in from a FCS file header). It lists the keywords and its values
for a flowFrame specified by a character vector. Additional methods for
function and lists exists for more programmatic access to the
keywords.
keyword(object, keyword, ...)
| object | Object of class |
|---|---|
| keyword | Character vector or list of potential keywords or function. If missing all keywords are returned. |
| ... | compact: logical scaler to indicate whether to hide all the cytometer instrument and laser settings from keywords. |
The keyword methods allow access to the keywords stored in the FCS
files, either for a flowFrame or for a list of frames in a
flowSet. The most simple use case is to provide a character vector or
a list of character strings of keyword names. A more sophisticated version
is to provide a function which has to take one mandatory argument, the value
of this is the flowFrame. This can be used to query arbitrary
information from the flowFrames description slot or even the
raw data. The function has to return a single character string. The
list methods allow to combine functional and direct keyword access.
The replacement method takes a named character vector or a named list as
input.
Return values for
all keywords from the description slot in object that match
the character vector keyword.
Apply the function in
keyword on the flowFrame object. The function
needs to be able to cope with a single argument and it needs to return a
single character string. A typical use case is for instance to paste
together values from several different keywords or to compute some statistic
on the flowFrame and combine it with one or several other keywords.
Combine characters and functions in a list to select keyword values.
This is essentially an
alias for description and returns all keyword-value pairs.
This is a wrapper around
fsApply(object, keyword, keyword) which essentially iterates over the
frames in the flowSet.
This first coerces the
keyword (mostly a character vector) to a list and then calls the next
applicable method.
#> $FCSversion #> [1] "2" #> #> $`$BYTEORD` #> [1] "4,3,2,1" #> #> $`$DATATYPE` #> [1] "F" #> #> $`$NEXTDATA` #> [1] "0" #> #> $`$SYS` #> [1] "Macintosh System Software 9.2.2" #> #> $CREATOR #> [1] "CELLQuest<aa> 3.3" #> #> $`$TOT` #> [1] "10000" #> #> $`$MODE` #> [1] "L" #> #> $`$PAR` #> [1] "8" #> #> $`$P1N` #> [1] "FSC-H" #> #> $`$P1R` #> [1] "1024" #> #> $`$P1B` #> [1] "16" #> #> $`$P1E` #> [1] "0,0" #> #> $`$P2N` #> [1] "SSC-H" #> #> $`$P2R` #> [1] "1024" #> #> $`$P2B` #> [1] "16" #> #> $`$P2E` #> [1] "0,0" #> #> $`$P3N` #> [1] "FL1-H" #> #> $`$P3R` #> [1] "1024" #> #> $`$P3B` #> [1] "16" #> #> $`$P3E` #> [1] "0,0" #> #> $`$P4N` #> [1] "FL2-H" #> #> $`$P4R` #> [1] "1024" #> #> $`$P4B` #> [1] "16" #> #> $`$P4E` #> [1] "0,0" #> #> $`$P5N` #> [1] "FL3-H" #> #> $`$P5R` #> [1] "1024" #> #> $`$P5B` #> [1] "16" #> #> $`$P5E` #> [1] "0,0" #> #> $`$P1S` #> [1] "FSC-H" #> #> $`$P2S` #> [1] "SSC-H" #> #> $`$P3S` #> character(0) #> #> $`$P4S` #> character(0) #> #> $`$P6N` #> [1] "FL1-A" #> #> $`$P6R` #> [1] "1024" #> #> $`$P6B` #> [1] "16" #> #> $`$P6E` #> [1] "0,0" #> #> $TIMETICKS #> [1] "50" #> #> $`$P7N` #> [1] "FL4-H" #> #> $`$P7R` #> [1] "1024" #> #> $`$P7E` #> [1] "0,0" #> #> $`$P7B` #> [1] "16" #> #> $`$P8N` #> [1] "Time" #> #> $`$P8R` #> [1] "1024" #> #> $`$P8E` #> [1] "0,0" #> #> $`$P8B` #> [1] "16" #> #> $`$P8S` #> [1] "Time (51.20 sec.)" #> #> $`SAMPLE ID` #> [1] "Default Patient ID" #> #> $`$SRC` #> [1] "Default Patient Name" #> #> $`CASE NUMBER` #> [1] "Default Case Number" #> #> $`$CYT` #> [1] "FACSCalibur" #> #> $CYTNUM #> [1] "E5451" #> #> $`$BTIM` #> [1] "13:13:54" #> #> $`$ETIM` #> [1] "13:14:27" #> #> $`BD$AcqLibVersion` #> [1] "3.1" #> #> $`BD$NPAR` #> [1] "7" #> #> $`BD$P1N` #> [1] "FSC-H" #> #> $`BD$P2N` #> [1] "SSC-H" #> #> $`BD$P3N` #> [1] "FL1-H" #> #> $`BD$P4N` #> [1] "FL2-H" #> #> $`BD$P5N` #> [1] "FL3-H" #> #> $`BD$P6N` #> [1] "FL1-A" #> #> $`BD$P7N` #> [1] "FL4-H" #> #> $`BD$WORD0` #> [1] "24" #> #> $`BD$WORD1` #> [1] "474" #> #> $`BD$WORD2` #> [1] "594" #> #> $`BD$WORD3` #> [1] "530" #> #> $`BD$WORD4` #> [1] "700" #> #> $`BD$WORD5` #> [1] "402" #> #> $`BD$WORD6` #> [1] "401" #> #> $`BD$WORD7` #> [1] "401" #> #> $`BD$WORD8` #> [1] "402" #> #> $`BD$WORD9` #> [1] "401" #> #> $`BD$WORD10` #> [1] "299" #> #> $`BD$WORD11` #> [1] "287" #> #> $`BD$WORD12` #> [1] "557" #> #> $`BD$WORD13` #> [1] "0" #> #> $`BD$WORD14` #> [1] "483" #> #> $`BD$WORD15` #> [1] "612" #> #> $`BD$WORD16` #> [1] "546" #> #> $`BD$WORD17` #> [1] "724" #> #> $`BD$WORD18` #> [1] "104" #> #> $`BD$WORD19` #> [1] "100" #> #> $`BD$WORD20` #> [1] "100" #> #> $`BD$WORD21` #> [1] "100" #> #> $`BD$WORD22` #> [1] "100" #> #> $`BD$WORD23` #> [1] "1" #> #> $`BD$WORD24` #> [1] "1" #> #> $`BD$WORD25` #> [1] "0" #> #> $`BD$WORD26` #> [1] "0" #> #> $`BD$WORD27` #> [1] "0" #> #> $`BD$WORD28` #> [1] "136" #> #> $`BD$WORD29` #> [1] "77" #> #> $`BD$WORD30` #> [1] "52" #> #> $`BD$WORD31` #> [1] "52" #> #> $`BD$WORD32` #> [1] "52" #> #> $`BD$WORD33` #> [1] "52" #> #> $`BD$WORD34` #> [1] "6" #> #> $`BD$WORD35` #> [1] "300" #> #> $`BD$WORD36` #> [1] "0" #> #> $`BD$WORD37` #> [1] "191" #> #> $`BD$WORD38` #> [1] "280" #> #> $`BD$WORD39` #> [1] "3" #> #> $`BD$WORD40` #> [1] "2" #> #> $`BD$WORD41` #> [1] "100" #> #> $`BD$WORD42` #> [1] "100" #> #> $`BD$WORD43` #> [1] "0" #> #> $`BD$WORD44` #> [1] "1023" #> #> $`BD$WORD45` #> [1] "1023" #> #> $`BD$WORD46` #> [1] "1023" #> #> $`BD$WORD47` #> [1] "53" #> #> $`BD$WORD48` #> [1] "721" #> #> $`BD$WORD49` #> [1] "127" #> #> $`BD$WORD50` #> [1] "22" #> #> $`BD$WORD51` #> [1] "52" #> #> $`BD$WORD52` #> [1] "0" #> #> $`BD$WORD53` #> [1] "0" #> #> $`BD$WORD54` #> [1] "0" #> #> $`BD$WORD55` #> [1] "0" #> #> $`BD$WORD56` #> [1] "0" #> #> $`BD$WORD57` #> [1] "0" #> #> $`BD$WORD58` #> [1] "0" #> #> $`BD$WORD59` #> [1] "0" #> #> $`BD$WORD60` #> [1] "0" #> #> $`BD$WORD61` #> [1] "0" #> #> $`BD$WORD62` #> [1] "0" #> #> $`BD$WORD63` #> [1] "0" #> #> $`BD$LASERMODE` #> [1] "1" #> #> $CalibFile #> [1] "FALSE" #> #> $P7THRESVOL #> [1] "52" #> #> $`$FIL` #> [1] "0877408774.B08" #> #> $`$DATE` #> [1] "03-Feb-06" #> #> $`NUMBER WELL INFO KEYWORDS` #> [1] "0" #> #> $`$P5S` #> character(0) #> #> $`$P7S` #> character(0) #> #> $`&1Sample Vol` #> [1] "200" #> #> $`&2Number of Washes` #> [1] "1" #> #> $`&3Mixing Vol` #> [1] "100" #> #> $`&4Number of Mixes` #> [1] "1" #> #> $`&5Data File Prefix Part #1` #> [1] "08774" #> #> $`&6Data File Prefix Part #2` #> [1] "08774" #> #> $`&7Data File Prefix Part #3` #> character(0) #> #> $`&8Acquisition Doc.` #> [1] "UDCP Acquisition Template" #> #> $`&9Instr. Sett. File` #> [1] "020306 InstrSettings" #> #> $`&10Analysis Doc.` #> character(0) #> #> $FILENAME #> [1] "/tmp/RtmpOnztbL/temp_libpath9122ee80e77/flowCore/extdata/0877408774.B08" #> #> $transformation #> [1] "applied" #> #> $`flowCore_$P1Rmax` #> [1] "1024" #> #> $`flowCore_$P1Rmin` #> [1] "0" #> #> $`flowCore_$P2Rmax` #> [1] "1024" #> #> $`flowCore_$P2Rmin` #> [1] "0" #> #> $`flowCore_$P3Rmax` #> [1] "10001" #> #> $`flowCore_$P3Rmin` #> [1] "1" #> #> $`flowCore_$P4Rmax` #> [1] "10001" #> #> $`flowCore_$P4Rmin` #> [1] "1" #> #> $`flowCore_$P5Rmax` #> [1] "10001" #> #> $`flowCore_$P5Rmin` #> [1] "1" #> #> $`flowCore_$P6Rmax` #> [1] "1024" #> #> $`flowCore_$P6Rmin` #> [1] "0" #> #> $`flowCore_$P7Rmax` #> [1] "10001" #> #> $`flowCore_$P7Rmin` #> [1] "1" #> #> $`flowCore_$P8Rmax` #> [1] "1024" #> #> $`flowCore_$P8Rmin` #> [1] "0" #> #> $GUID #> [1] "0877408774.B08" #>keyword(samp, compact = TRUE)#> $TIMETICKS #> [1] "50" #> #> $`SAMPLE ID` #> [1] "Default Patient ID" #> #> $`CASE NUMBER` #> [1] "Default Case Number" #> #> $CYTNUM #> [1] "E5451" #> #> $CalibFile #> [1] "FALSE" #> #> $`NUMBER WELL INFO KEYWORDS` #> [1] "0" #> #> $`&1Sample Vol` #> [1] "200" #> #> $`&2Number of Washes` #> [1] "1" #> #> $`&3Mixing Vol` #> [1] "100" #> #> $`&4Number of Mixes` #> [1] "1" #> #> $`&5Data File Prefix Part #1` #> [1] "08774" #> #> $`&6Data File Prefix Part #2` #> [1] "08774" #> #> $`&7Data File Prefix Part #3` #> character(0) #> #> $`&8Acquisition Doc.` #> [1] "UDCP Acquisition Template" #> #> $`&9Instr. Sett. File` #> [1] "020306 InstrSettings" #> #> $`&10Analysis Doc.` #> character(0) #> #> $FILENAME #> [1] "/tmp/RtmpOnztbL/temp_libpath9122ee80e77/flowCore/extdata/0877408774.B08" #> #> $transformation #> [1] "applied" #> #> $GUID #> [1] "0877408774.B08" #>keyword(samp, "FCSversion")#> $FCSversion #> [1] "2" #>#> [1] "Default Patient ID_0877408774.B08"keyword(samp)[["foo"]] <- "bar" data(GvHD) keyword(GvHD, list("GUID", cellnumber=function(x) nrow(x)))#> cellnumber #> s5a01 3420 #> s5a02 3405 #> s5a03 3435 #> s5a04 8550 #> s5a05 10410 #> s5a06 3750 #> s5a07 13979 #> s6a01 2205 #> s6a02 13350 #> s6a03 11610 #> s6a04 13830 #> s6a05 13934 #> s6a06 19470 #> s6a07 9405 #> s7a01 16055 #> s7a02 10305 #> s7a03 30195 #> s7a04 59849 #> s7a05 39068 #> s7a06 11939 #> s7a07 13214 #> s9a01 12666 #> s9a02 8265 #> s9a03 4065 #> s9a04 7080 #> s9a05 66105 #> s9a06 49421 #> s9a07 12768 #> s10a01 17289 #> s10a02 4530 #> s10a03 6765 #> s10a04 9540 #> s10a05 25515 #> s10a06 24656 #> s10a07 25601