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1 This package contains R code for converting and transforming a binary
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2 FCS file, using the FCSTrans software, and the C code for running the
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3 flock1 and flock2 population identification software.
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4
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5 src - contains the C code for flock1, flock2 and cent_adjust
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6 bin - contains the compiled C code for flock1, flock2 and cent_adjust,
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7 plus the R code for using the FCSTrans algorithm for file
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8 conversion and data transformation.
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9 doc - documentation for FCSTrans and FLOCK algorithms
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10 example - sample data and output from FCSTrans and FLOCK
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11
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12 To run this software sucessfully the code assumes the software was installed
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13 in the /usr/local/flock directory and that R, plus the Bioconductor flowCore
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14 module has been installed. If you use the ipconvert.sh shell script, you
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15 may need to adjust the location of the RScript executable and the location
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16 of the FCSTrans.R code by editing the shell script.
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17
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18 #############################################################################
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19 # Overview
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20 #############################################################################
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21 ImmPort-FLOCK
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22
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23 FLOCK (FLOw Clustering without K), an automated population discovery tool for
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24 multidimensional FCM data was designed to specifically take into account the
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25 unique feature of FCM data and produce objective segregation of cell
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26 populations.
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27
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28 FLOCK parameter settings can be customized by defining Bins and Density
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29 Threshold. The number of bins is an integer specifying the number of
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30 equal-sized regions the data will be partitioned into on each axis. Increasing
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31 the number of bins increases the sensitivity to detect rare populations but
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32 may also result in single populations being divided. Density Threshold is the
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33 cut-off value to separate the dense regions from background. It is a floating
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34 point number that helps define population centers; increasing the threshold
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35 may help separate major populations but could cause the algorithm to overlook
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36 rare populations.
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37
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38 #############################################################################
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39 # Compiling C code
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40 #############################################################################
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41 cd bin
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42 cc -o flock1 ../src/flock1.c ../src/find_connected.c -lm
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43 cc -o flock2 ../src/flock2.c -lm
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44 cc -o cent_adjust ../src/cent_adjust.c -lm
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45
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46 #############################################################################
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47 # FCSTrans
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48 #############################################################################
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49 A shell script named ipconvert.sh is included that runs the FCSTrans R
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50 code for converting and transforming a binary FCS file. The output consists
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51 of one text file containing the transformed channel intensity values and
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52 another file containing a list of the FCS parameters.
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53
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54 cd bin
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55 /usr/local/flock/bin/ipconvert.sh ../example/data/FCS2.fcs
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56 /usr/local/flock/bin/ipconvert.sh ../example/data/FCS3.fcs
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57
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58 #############################################################################
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59 # Running flock1 or flock2
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60 #############################################################################
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61 Running the FLOCK1 and FLOCK2 algorithms generate 8 output files that have
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62 generic file names. For this reason, it is recommended that one output
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63 directory be created for one input file to the program.
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64
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65 cd example/output/FCS2
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66 /usr/local/flock/bin/flock1 ../../data/FCS2.txt
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67
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68 cd example/output/FCS3
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69 /usr/local/flock/bin/flock2 ../../data/FCS3.txt
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70
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71 Files created: MFI.txt, percentage.txt, population_id.txt, profile.txt,
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72 flock_results.txt, coordinates.txt, population_center.txt
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73 and percentage.txt
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74
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75 Usage Information for FLOCK1
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76 ----------------------------------------------------------------------------
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77 basic mode: flock1 fcs.txt
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78 advanced_ mode: flock1 fcs.txt num_bin density_index max_num_pop
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79
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80 Usage Information for FLOCK2
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81 ----------------------------------------------------------------------------
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82 basic mode: flock data_file
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83 advanced mode 0 (specify maximum # of pops): flock data_file max_num_pop
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84 advanced mode 1 (without # of pops): flock data_file num_bin density_index
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85 advanced mode 2 (specify # of pops): flock data_file num_bin density_index
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86 number_of_pop
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87 advanced mode 3 (specify both # of pops): flock data_file num_bin density_index
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88 number_of_pop max_num_pop
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89
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90 FLOCK Output Files
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91 ----------------------------------------------------------------------------
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92 coordinates.txt:
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93 Output is the intensity values for each marker and event
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94
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95 flock_results.txt:
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96 A combination of the input file, event identifiers and population
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97 identifiers.
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98
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99 MFI.txt:
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100 Provides the mean fluorescence intensity for each population for each
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101 marker/parameter
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102
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103 population_id.txt:
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104 Contains population identifiers (i.e, values from [1 to n] where n is
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105 the population assigned to the corresponding events in the input data
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106 file, one identifier per row.)
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107
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108 population_center.txt:
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109 Contains the centroid coordinates for each identified population
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110
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111 percentage.txt:
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112 Includes the population identifiers and percentage of events within that
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113 population (relative to the whole data file)
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114
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115 profile.txt:
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116 Displays an expression profile, where the approximate expression level
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117 for each marker is assigned a numeric value from 1-4, for each identified
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118 population
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119
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120 fcs_properties.txt:
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121 Contains the number of events, number of populations, and number of
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122 markers, as well as the algorithm parameters used in the analysis
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123
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124 #############################################################################
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125 # Running cent_adjust
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126 #############################################################################
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127 Running the cent_adjust algorithm generates 4 output files that have
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128 generic file names. For this reason, it is recommened that one output
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129 directory be created for one input file to the program.
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130
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131 mkdir example/output/FCS2/cent_adjust
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132 cd example/output/FCS2/cent_adjust
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133 /usr/local/flock/bin/cent_adjust ../population_center.txt ../coordinates.txt
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134
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135 Files created: MFI.txt, percentage.txt, population_id.txt and profile.txt
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136
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137 Usage Information for cent_adjust
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138 ----------------------------------------------------------------------------
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139 basic mode: cent_adjust input_center input_data_file
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