SeekTest

Usage

Basic Usage

 SeekTest -i <genes.txt> -x <db list> -d <input directory> -D <output_dir>

Detailed Usage

package "SeekTest"
version "1.0"
purpose "Statistical test on a gene set for a given dataset"

section "Mode"
option  "dab"               D   "DAB mode"
                                flag    off
option  "bin"               A   "PCL Bin mode"
                                flag    off
option  "db"                d   "DB mode"
                                flag    off

section "DB mode"
option  "db_dir"            E   "DB directory"
                                string typestr="directory"
option  "db_num"            b   "Number of files in DB directory"
                                int default="1000"
option  "prep"              P   "Prep directory (containing .gavg and .gpres files)"
                                string typestr="filename"
option  "sinfo"             s   "Sinfo directory (containing .sinfo files)"
                                string typestr="filename"
option  "dataset_list"      C   "Dataset list"
                                string typestr="filename"
option  "query"             Q   "List of genes separated by spaces in one line"
                                string typestr="filename"
option  "quant"             q   "Quant file"
                                string typestr="filename"
option  "count_pair"        c   "Count number of z-scores exceeding a threshold"
                                flag    off
option  "histogram"         h   "Get distribution of z-scores of given genes"
                                flag    off

section "DAB mode"
option  "gene_set_list"     g   "List of gene-set files"
                                string typestr="filename"
option  "input"             x   "Gene mapping file"
                                string typestr="filename"
option  "dabinput"          B   "DAB dataset file"
                                string typestr="filename"
option  "gavg_input"        a   "Gene average (.gavg) input file"
                                string typestr="filename"
option  "gpres_input"       p   "Gene presence (.gpres) input file"
                                string typestr="filename"

Flag	Default	Type	Description
-i	stdin	Text file	Tab-delimited text file containing two columns, numerical gene IDs (one-based) and unique gene names (matching those in the input DAT/DAB files).
-d	.	Directory	Input directory containing DB files
-D	.	Directory	Output directory in which database files will be stored.
-x	.	Text file	Input file containing list of CDatabaselets to combine