read.FCSheader.RdRead (part of) the TEXT section of a Data File Standard for Flow Cytometry that contains FACS keywords.
read.FCSheader(files, path = ".", keyword = NULL, ...)
| files | Character vector of filenames. |
|---|---|
| path | Directory where to look for the files. |
| keyword | An optional character vector that specifies the FCS keyword to read. |
| ... | other arguments passed to |
A list of character vectors. Each element of the list correspond to one FCS file.
The function read.FCSheader works with the output of the FACS machine
software from a number of vendors (FCS 2.0, FCS 3.0 and List Mode Data LMD).
The output of the function is the TEXT section of the FCS files. The user
can specify some keywords to limit the output to the information of
interest.
link[flowCore]{read.flowSet},
link[flowCore]{read.FCS}
#> $`/tmp/RtmpOnztbL/temp_libpath9122ee80e77/flowCore/extdata/0877408774.B08` #> FCSversion $BYTEORD #> "2" "4,3,2,1" #> $DATATYPE $NEXTDATA #> "I" "0" #> $SYS CREATOR #> "Macintosh System Software 9.2.2" "CELLQuest<aa> 3.3" #> $TOT $MODE #> "10000" "L" #> $PAR $P1N #> "8" "FSC-H" #> $P1R $P1B #> "1024" "16" #> $P1E $P2N #> "0,0" "SSC-H" #> $P2R $P2B #> "1024" "16" #> $P2E $P3N #> "0,0" "FL1-H" #> $P3R $P3B #> "1024" "16" #> $P3E $P4N #> "4,1" "FL2-H" #> $P4R $P4B #> "1024" "16" #> $P4E $P5N #> "4,1" "FL3-H" #> $P5R $P5B #> "1024" "16" #> $P5E $P1S #> "4,1" "FSC-H" #> $P2S $P3S #> "SSC-H" "" #> $P4S $P6N #> "" "FL1-A" #> $P6R $P6B #> "1024" "16" #> $P6E TIMETICKS #> "0,0" "50" #> $P7N $P7R #> "FL4-H" "1024" #> $P7E $P7B #> "4,1" "16" #> $P8N $P8R #> "Time" "1024" #> $P8E $P8B #> "0,0" "16" #> $P8S SAMPLE ID #> "Time (51.20 sec.)" "Default Patient ID" #> $SRC CASE NUMBER #> "Default Patient Name" "Default Case Number" #> $CYT CYTNUM #> "FACSCalibur" "E5451" #> $BTIM $ETIM #> "13:13:54" "13:14:27" #> BD$AcqLibVersion BD$NPAR #> "3.1" "7" #> BD$P1N BD$P2N #> "FSC-H" "SSC-H" #> BD$P3N BD$P4N #> "FL1-H" "FL2-H" #> BD$P5N BD$P6N #> "FL3-H" "FL1-A" #> BD$P7N BD$WORD0 #> "FL4-H" "24" #> BD$WORD1 BD$WORD2 #> "474" "594" #> BD$WORD3 BD$WORD4 #> "530" "700" #> BD$WORD5 BD$WORD6 #> "402" "401" #> BD$WORD7 BD$WORD8 #> "401" "402" #> BD$WORD9 BD$WORD10 #> "401" "299" #> BD$WORD11 BD$WORD12 #> "287" "557" #> BD$WORD13 BD$WORD14 #> "0" "483" #> BD$WORD15 BD$WORD16 #> "612" "546" #> BD$WORD17 BD$WORD18 #> "724" "104" #> BD$WORD19 BD$WORD20 #> "100" "100" #> BD$WORD21 BD$WORD22 #> "100" "100" #> BD$WORD23 BD$WORD24 #> "1" "1" #> BD$WORD25 BD$WORD26 #> "0" "0" #> BD$WORD27 BD$WORD28 #> "0" "136" #> BD$WORD29 BD$WORD30 #> "77" "52" #> BD$WORD31 BD$WORD32 #> "52" "52" #> BD$WORD33 BD$WORD34 #> "52" "6" #> BD$WORD35 BD$WORD36 #> "300" "0" #> BD$WORD37 BD$WORD38 #> "191" "280" #> BD$WORD39 BD$WORD40 #> "3" "2" #> BD$WORD41 BD$WORD42 #> "100" "100" #> BD$WORD43 BD$WORD44 #> "0" "1023" #> BD$WORD45 BD$WORD46 #> "1023" "1023" #> BD$WORD47 BD$WORD48 #> "53" "721" #> BD$WORD49 BD$WORD50 #> "127" "22" #> BD$WORD51 BD$WORD52 #> "52" "0" #> BD$WORD53 BD$WORD54 #> "0" "0" #> BD$WORD55 BD$WORD56 #> "0" "0" #> BD$WORD57 BD$WORD58 #> "0" "0" #> BD$WORD59 BD$WORD60 #> "0" "0" #> BD$WORD61 BD$WORD62 #> "0" "0" #> BD$WORD63 BD$LASERMODE #> "0" "1" #> CalibFile P7THRESVOL #> "FALSE" "52" #> $FIL $DATE #> "0877408774.B08" "03-Feb-06" #> NUMBER WELL INFO KEYWORDS $P5S #> "0" "" #> $P7S &1Sample Vol #> "" "200" #> &2Number of Washes &3Mixing Vol #> "1" "100" #> &4Number of Mixes &5Data File Prefix Part #1 #> "1" "08774" #> &6Data File Prefix Part #2 &7Data File Prefix Part #3 #> "08774" "" #> &8Acquisition Doc. &9Instr. Sett. File #> "UDCP Acquisition Template" "020306 InstrSettings" #> &10Analysis Doc. #> "" #>samp <- read.FCSheader(system.file("extdata", "0877408774.B08", package="flowCore"), keyword=c("$DATE", "$FIL")) samp#> $`/tmp/RtmpOnztbL/temp_libpath9122ee80e77/flowCore/extdata/0877408774.B08` #> $DATE $FIL #> "03-Feb-06" "0877408774.B08" #>