| FUNCTION | SHORT DESCRIPTION |
| MANHATTAN | Manhattan plot maker. |
This function generates Manhattan plots. It is possible to select any number of chromosomes. If one chromosome is selected you can zoom in on a specified region. Any input file that has chromsome number, position and p-value can be used. File must be sorted by chromsome number and each chromosome by position number (most GWAS output files already are)! No missing chromsosome or position values tolerated; p-values can be missing. Any delimiter supported (but must be defined), header allowed (can be of any size) and optional. The values below a specified threshold are also written into a file.
Note:If you want to use this script on the UT cluster with Slurm you need to use xvfb (example: "xvfb-run /gpfs/gvgpfs/gvhome/toomasha/SOFT/LFG64 ") or use the -Y tag with ssh (example: "ssh -Y user@address").
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./LFG32 -M manhattan -file -column -idcolumn -poscolumn -out -delim -header -header-size -chr -posrange -missing -threshold -figuretitle -xnum -ynum -font1 -font2 -div |
-file = filename. REQUIRED.
-column = p-value column number. Options: valid column number. REQUIRED
-idcolumn = chromsome column number. Options: valid column number. REQUIRED
-poscolumn = position column number. Options: valid column number. REQUIRED
-out = output file name where p-values go (use without extension). Options: any name. Default = input file name modified
-delim = file delimiter. Options: a) "tab", "space", "colon", "semicolon", b) any symbol or word without spaces (some symbols require that you precede them with "\"). Default = "tab".
-header = file header. Options: "yes", "no". Default = "no".
-header-size = file header size (# of rows); use only if header is larger than 1 row; only the last row is used in the output file. Options: any integer. Default = 1
-chr = what chromosomes to include. Options: separate chromosomes by "," use "-" for ranges. Example = 1,3,7-11.
-posrange = if one chromosome is used you can define a range. Example = 2000000-9000000
-missing = value used for missing p-values. Default = NA
-threshold = this is -log10(PVALUE); the values larger than this will become red in the graph and are printed into a file. Default = 7.3 (corresponds to P=5E-8)
-figuretitle = a way the specify title for the figure. Default = input file name
-xnum = every which chromosome is numbered. Default = 1, recommend 2
-ynum = every which value is shown for the y axis. Default = 1, recommend 2
-font1 = font size of the title. Default = 12
-font2 = font size of the axis values. Default = 10
-div = used if the physical numbers of the x-axis are very large and the memory cannot handle the values; does not affect the outcome in any way but changes how the script generates the outcome. Example: -div 100 (use this for very large values)
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Example (minimal): ./LFG32 -M manhattan -file table.txt -column 1 -idcolumn 2 -poscolumn 3 -out results The input file has no header, is tab delimited, all columns are included with default values. Example (maximal): ./LFG32 -M manhattan -file table.txt -column 1 -idcolumn 2 -poscolumn 3 -out results -delim space -header yes -header-size 14 -chr 1 -posrange 6000000-9000000 -missing na -threshold 6.5 -figuretitle My_Manhatan -xnum 2 -ynum 2 -font1 14 -font2 12 -div 100 The input file has a header (header size = 14, only the last header row is written into the output file), is space delimited, only a specific range from chromsome one is displayed. |