|
Biorithm
1.1
|
|
Biorithm
1.1
|
Where the command line options are stored. More...
#include <cmdline.h>
Public Attributes | |
| const char * | help_help |
| Print help and exit help description. | |
| const char * | version_help |
| Print version and exit help description. | |
| float | alpha_arg |
| minimum size of cluster/number of points (default='0'). | |
| char * | alpha_orig |
| minimum size of cluster/number of points original value given at command line. | |
| const char * | alpha_help |
| minimum size of cluster/number of points help description. | |
| int | anneal_flag |
| do simulated annealing to improve clusters (default=off). | |
| const char * | anneal_help |
| do simulated annealing to improve clusters help description. | |
| int | apriori_flag |
| compute itemsets using the apriori algorithm (default=off). | |
| const char * | apriori_help |
| compute itemsets using the apriori algorithm help description. | |
| char * | classes_arg |
| input file for class information (default=''). | |
| char * | classes_orig |
| input file for class information original value given at command line. | |
| const char * | classes_help |
| input file for class information help description. | |
| char * | config_arg |
| file containing parameters and configuration information (default=''). | |
| char * | config_orig |
| file containing parameters and configuration information original value given at command line. | |
| const char * | config_help |
| file containing parameters and configuration information help description. | |
| float | correlations_arg |
| Compute correlations between pairs of genes using the argument as the threshold. If the absolute value of the threshold is at least 1 and less than 2, compute a histogram of all the correlations. If the absolute value of the threshold is at least two, compute a histogram of all the correlations by randomising the dataset; the absolute value of the threshold indicates the number of times to randomise. (default='1'). | |
| char * | correlations_orig |
| Compute correlations between pairs of genes using the argument as the threshold. If the absolute value of the threshold is at least 1 and less than 2, compute a histogram of all the correlations. If the absolute value of the threshold is at least two, compute a histogram of all the correlations by randomising the dataset; the absolute value of the threshold indicates the number of times to randomise. original value given at command line. | |
| const char * | correlations_help |
| Compute correlations between pairs of genes using the argument as the threshold. If the absolute value of the threshold is at least 1 and less than 2, compute a histogram of all the correlations. If the absolute value of the threshold is at least two, compute a histogram of all the correlations by randomising the dataset; the absolute value of the threshold indicates the number of times to randomise. help description. | |
| int | flip_flag |
| flip points and coordinates (default=on). | |
| const char * | flip_help |
| flip points and coordinates help description. | |
| int | filter_flag |
| filter data (default=off). | |
| const char * | filter_help |
| filter data help description. | |
| int | gibbs_flag |
| run Gibbs sampling (default=off). | |
| const char * | gibbs_help |
| run Gibbs sampling help description. | |
| int | greedy_flag |
| find clusters using a greedy algorithm (default=off). | |
| const char * | greedy_help |
| find clusters using a greedy algorithm help description. | |
| char * | generate_arg |
| output file for randomly generated clusters (default=''). | |
| char * | generate_orig |
| output file for randomly generated clusters original value given at command line. | |
| const char * | generate_help |
| output file for randomly generated clusters help description. | |
| char * | input_arg |
| input file for points and coordinates (default=''). | |
| char * | input_orig |
| input file for points and coordinates original value given at command line. | |
| const char * | input_help |
| input file for points and coordinates help description. | |
| int | itemsets_flag |
| compute frequent itemsets in the data (default=off). | |
| const char * | itemsets_help |
| compute frequent itemsets in the data help description. | |
| char * | limit_arg |
| input file for limiting xMotifs (for constrained biclustering) (default=''). | |
| char * | limit_orig |
| input file for limiting xMotifs (for constrained biclustering) original value given at command line. | |
| const char * | limit_help |
| input file for limiting xMotifs (for constrained biclustering) help description. | |
| int | memory_flag |
| conserve memory used (default=on). | |
| const char * | memory_help |
| conserve memory used help description. | |
| int | min_flag |
| minimise the size of the xMotifs (default=off). | |
| const char * | min_help |
| minimise the size of the xMotifs help description. | |
| int | number_arg |
| number of samples or genes to read (default='-1'). | |
| char * | number_orig |
| number of samples or genes to read original value given at command line. | |
| const char * | number_help |
| number of samples or genes to read help description. | |
| char * | output_arg |
| output results to file (default=''). | |
| char * | output_orig |
| output results to file original value given at command line. | |
| const char * | output_help |
| output results to file help description. | |
| int | partition_flag |
| compute disjoint xMotifs (default=on). | |
| const char * | partition_help |
| compute disjoint xMotifs help description. | |
| int | significant_flag |
| should every bounded dimension of a projective cluster be significant? (default=on). | |
| const char * | significant_help |
| should every bounded dimension of a projective cluster be significant? help description. | |
| int | statistics_flag |
| output statistics on the sizes of computed xMotifs. This option is useful for estimating the significance of xMotifs in real data. (default=off). | |
| const char * | statistics_help |
| output statistics on the sizes of computed xMotifs. This option is useful for estimating the significance of xMotifs in real data. help description. | |
| int | test_flag |
| execute tests (default=off). | |
| const char * | test_help |
| execute tests help description. | |
| int | train_flag |
| train the classifier (default=off). | |
| const char * | train_help |
| train the classifier help description. | |
| int | verbose_arg |
| print a lot of information about the results (default='1'). | |
| char * | verbose_orig |
| print a lot of information about the results original value given at command line. | |
| const char * | verbose_help |
| print a lot of information about the results help description. | |
| float | width_arg |
| maximum width of a bounded dimension (default='0'). | |
| char * | width_orig |
| maximum width of a bounded dimension original value given at command line. | |
| const char * | width_help |
| maximum width of a bounded dimension help description. | |
| int | gaussian_flag |
| use gaussian distribution as assumption for calculating significant intervals (default=off). | |
| const char * | gaussian_help |
| use gaussian distribution as assumption for calculating significant intervals help description. | |
| char * | genes_arg |
| read genes to use from file (default=''). | |
| char * | genes_orig |
| read genes to use from file original value given at command line. | |
| const char * | genes_help |
| read genes to use from file help description. | |
| char * | gene_id_column_arg |
| name of column containing gene/probe ids (default=''). | |
| char * | gene_id_column_orig |
| name of column containing gene/probe ids original value given at command line. | |
| const char * | gene_id_column_help |
| name of column containing gene/probe ids help description. | |
| char * | gene_name_column_arg |
| name of column containing gene names (default=''). | |
| char * | gene_name_column_orig |
| name of column containing gene names original value given at command line. | |
| const char * | gene_name_column_help |
| name of column containing gene names help description. | |
| char * | ignore_column_name_arg |
| name of column to ignore (default=''). | |
| char * | ignore_column_name_orig |
| name of column to ignore original value given at command line. | |
| const char * | ignore_column_name_help |
| name of column to ignore help description. | |
| char * | ignore_row_name_arg |
| name of row to ignore (default=''). | |
| char * | ignore_row_name_orig |
| name of row to ignore original value given at command line. | |
| const char * | ignore_row_name_help |
| name of row to ignore help description. | |
| float | lb_arg |
| lower threshold to use when filtering (default='1'). | |
| char * | lb_orig |
| lower threshold to use when filtering original value given at command line. | |
| const char * | lb_help |
| lower threshold to use when filtering help description. | |
| int | log_flag |
| transform points by taking logarithms per gene (default=off). | |
| const char * | log_help |
| transform points by taking logarithms per gene help description. | |
| int | mc_arg |
| maximum count of points in siginificant interval (default='-1'). | |
| char * | mc_orig |
| maximum count of points in siginificant interval original value given at command line. | |
| const char * | mc_help |
| maximum count of points in siginificant interval help description. | |
| float | mh_arg |
| minimum (class) homogeneity of a projective cluster (default='0'). | |
| char * | mh_orig |
| minimum (class) homogeneity of a projective cluster original value given at command line. | |
| const char * | mh_help |
| minimum (class) homogeneity of a projective cluster help description. | |
| float | min_up_regulated_arg |
| for cDNA or normalised microarray data, a gene is up-regulated if its expression value is at least this parameter (default='0'). | |
| char * | min_up_regulated_orig |
| for cDNA or normalised microarray data, a gene is up-regulated if its expression value is at least this parameter original value given at command line. | |
| const char * | min_up_regulated_help |
| for cDNA or normalised microarray data, a gene is up-regulated if its expression value is at least this parameter help description. | |
| float | max_down_regulated_arg |
| for cDNA or normalised microarray data, a gene is down-regulated if its expression value is at most this parameter (default='0'). | |
| char * | max_down_regulated_orig |
| for cDNA or normalised microarray data, a gene is down-regulated if its expression value is at most this parameter original value given at command line. | |
| const char * | max_down_regulated_help |
| for cDNA or normalised microarray data, a gene is down-regulated if its expression value is at most this parameter help description. | |
| int | nb_arg |
| number of best clusters to compute (default='1'). | |
| char * | nb_orig |
| number of best clusters to compute original value given at command line. | |
| const char * | nb_help |
| number of best clusters to compute help description. | |
| int | nc_arg |
| number of clusters to compute (default='-1'). | |
| char * | nc_orig |
| number of clusters to compute original value given at command line. | |
| const char * | nc_help |
| number of clusters to compute help description. | |
| int | nm_arg |
| number of motifs to compute (default='-2'). | |
| char * | nm_orig |
| number of motifs to compute original value given at command line. | |
| const char * | nm_help |
| number of motifs to compute help description. | |
| int | nd_arg |
| number of random discriminants (default='-1'). | |
| char * | nd_orig |
| number of random discriminants original value given at command line. | |
| const char * | nd_help |
| number of random discriminants help description. | |
| int | sd_arg |
| size of a discriminant (default='-1'). | |
| char * | sd_orig |
| size of a discriminant original value given at command line. | |
| const char * | sd_help |
| size of a discriminant help description. | |
| int | ns_arg |
| number of random seeds (default='1'). | |
| char * | ns_orig |
| number of random seeds original value given at command line. | |
| const char * | ns_help |
| number of random seeds help description. | |
| char * | oi_arg |
| output internal values to file (default=''). | |
| char * | oi_orig |
| output internal values to file original value given at command line. | |
| const char * | oi_help |
| output internal values to file help description. | |
| int | pc_arg |
| the maximum number of different xMotifs a sample can appear in (use with the -p option) (default='1'). | |
| char * | pc_orig |
| the maximum number of different xMotifs a sample can appear in (use with the -p option) original value given at command line. | |
| const char * | pc_help |
| the maximum number of different xMotifs a sample can appear in (use with the -p option) help description. | |
| float | pv_arg |
| maximum p-value to allow for interval (default='1'). | |
| char * | pv_orig |
| maximum p-value to allow for interval original value given at command line. | |
| const char * | pv_help |
| maximum p-value to allow for interval help description. | |
| char * | rf_arg |
| file containing ranges of widths for each gene/dimension (default=''). | |
| char * | rf_orig |
| file containing ranges of widths for each gene/dimension original value given at command line. | |
| const char * | rf_help |
| file containing ranges of widths for each gene/dimension help description. | |
| char * | row_name_column_arg |
| name of column containing row names (default=''). | |
| char * | row_name_column_orig |
| name of column containing row names original value given at command line. | |
| const char * | row_name_column_help |
| name of column containing row names help description. | |
| int | shamir_flag |
| run Sharon, Tanay, and Shamir's biclustering algorithm (default=off). | |
| const char * | shamir_help |
| run Sharon, Tanay, and Shamir's biclustering algorithm help description. | |
| float | st_arg |
| threshold for similarity of two xMotifs (they are similar if they have more than this fraction of points incommon). Use with the --nb option only. (default='0.5'). | |
| char * | st_orig |
| threshold for similarity of two xMotifs (they are similar if they have more than this fraction of points incommon). Use with the --nb option only. original value given at command line. | |
| const char * | st_help |
| threshold for similarity of two xMotifs (they are similar if they have more than this fraction of points incommon). Use with the --nb option only. help description. | |
| float | ub_arg |
| upper threshold to use when filtering (default='1'). | |
| char * | ub_orig |
| upper threshold to use when filtering original value given at command line. | |
| const char * | ub_help |
| upper threshold to use when filtering help description. | |
| int | uniform_flag |
| use uniform distribution as assumption for calculating significant intervals (default=off). | |
| const char * | uniform_help |
| use uniform distribution as assumption for calculating significant intervals help description. | |
| char * | wf_arg |
| file containing significant intervals for each gene/dimension (default=''). | |
| char * | wf_orig |
| file containing significant intervals for each gene/dimension original value given at command line. | |
| const char * | wf_help |
| file containing significant intervals for each gene/dimension help description. | |
| unsigned int | help_given |
| Whether help was given. | |
| unsigned int | version_given |
| Whether version was given. | |
| unsigned int | alpha_given |
| Whether alpha was given. | |
| unsigned int | anneal_given |
| Whether anneal was given. | |
| unsigned int | apriori_given |
| Whether apriori was given. | |
| unsigned int | classes_given |
| Whether classes was given. | |
| unsigned int | config_given |
| Whether config was given. | |
| unsigned int | correlations_given |
| Whether correlations was given. | |
| unsigned int | flip_given |
| Whether flip was given. | |
| unsigned int | filter_given |
| Whether filter was given. | |
| unsigned int | gibbs_given |
| Whether gibbs was given. | |
| unsigned int | greedy_given |
| Whether greedy was given. | |
| unsigned int | generate_given |
| Whether generate was given. | |
| unsigned int | input_given |
| Whether input was given. | |
| unsigned int | itemsets_given |
| Whether itemsets was given. | |
| unsigned int | limit_given |
| Whether limit was given. | |
| unsigned int | memory_given |
| Whether memory was given. | |
| unsigned int | min_given |
| Whether min was given. | |
| unsigned int | number_given |
| Whether number was given. | |
| unsigned int | output_given |
| Whether output was given. | |
| unsigned int | partition_given |
| Whether partition was given. | |
| unsigned int | significant_given |
| Whether significant was given. | |
| unsigned int | statistics_given |
| Whether statistics was given. | |
| unsigned int | test_given |
| Whether test was given. | |
| unsigned int | train_given |
| Whether train was given. | |
| unsigned int | verbose_given |
| Whether verbose was given. | |
| unsigned int | width_given |
| Whether width was given. | |
| unsigned int | gaussian_given |
| Whether gaussian was given. | |
| unsigned int | genes_given |
| Whether genes was given. | |
| unsigned int | gene_id_column_given |
| Whether gene-id-column was given. | |
| unsigned int | gene_name_column_given |
| Whether gene-name-column was given. | |
| unsigned int | ignore_column_name_given |
| Whether ignore-column-name was given. | |
| unsigned int | ignore_row_name_given |
| Whether ignore-row-name was given. | |
| unsigned int | lb_given |
| Whether lb was given. | |
| unsigned int | log_given |
| Whether log was given. | |
| unsigned int | mc_given |
| Whether mc was given. | |
| unsigned int | mh_given |
| Whether mh was given. | |
| unsigned int | min_up_regulated_given |
| Whether min-up-regulated was given. | |
| unsigned int | max_down_regulated_given |
| Whether max-down-regulated was given. | |
| unsigned int | nb_given |
| Whether nb was given. | |
| unsigned int | nc_given |
| Whether nc was given. | |
| unsigned int | nm_given |
| Whether nm was given. | |
| unsigned int | nd_given |
| Whether nd was given. | |
| unsigned int | sd_given |
| Whether sd was given. | |
| unsigned int | ns_given |
| Whether ns was given. | |
| unsigned int | oi_given |
| Whether oi was given. | |
| unsigned int | pc_given |
| Whether pc was given. | |
| unsigned int | pv_given |
| Whether pv was given. | |
| unsigned int | rf_given |
| Whether rf was given. | |
| unsigned int | row_name_column_given |
| Whether row-name-column was given. | |
| unsigned int | shamir_given |
| Whether shamir was given. | |
| unsigned int | st_given |
| Whether st was given. | |
| unsigned int | ub_given |
| Whether ub was given. | |
| unsigned int | uniform_given |
| Whether uniform was given. | |
| unsigned int | wf_given |
| Whether wf was given. | |
Where the command line options are stored.
1.7.6.1
