GSTAT(v1.0) is a collection of R functions for statistical analysis
of genome-wide data, by Qunyuan Zhang (qunyuan@wustl.edu), DSG. 
05-02-2009 updated


HOW TO USE (currently only available for GSC & DSG users)

TO USE THESE FUNCTIONS, INCLUDE THE LINE BELOW IN YOUR R SCRIPTS

-----------------------------------------
source("/gscmnt/sata180/info/medseq/biodb/shared/CancerGenomicTool/GDAC_statistical_packages/GSTAT/gstat.lib")
-----------------------------------------

######################
MUTATION ANALYSIS
######################

<SMG module: Significantly mutated gene test>

[FUNCTION] mutation_freq_test()
To test if mutation frequencies of genes or protein domains are significant 

[USAGE#1]
------------------------------------------------------------------------------------
mutation_freq_test(inf="input_data_file",outf="output_file",backgrd=0.000001)
------------------------------------------------------------------------------------
[DATA FORMAT]
Three columns, tab delimited (gene name, total mutation number, total bp length)
Example input_data_file "/gscuser/qzhang/gstat/example_data/mutation_data.csv"
[EXAMPLE RUN]
mutation_freq_test(inf="/gscuser/qzhang/gstat/example_data/mutation_data.csv",
outf="my_output_file.csv",backgrd=0.000001)
[NOTE]
You may specify you own backgrd value (i.e., backgroud mutaion frequency)

[USAGE#2]
------------------------------------------------------------------------------------
mutation_freq_test(inf="input_data_file",outf="output_file",option="protein")
------------------------------------------------------------------------------------
[DATA FORMAT]
Five columns, tab delimited (gene name, total mutation number of a protein domain, 
total mutation number of genes related to a protein domain,total bp length of protein domain,
total bp length of genes related to a protein domain)
Example input_data_file "/gscuser/qzhang/gstat/example_data/fmb.wbroad.csv"
[EXAMPLE RUN]
mutation_freq_test(inf="/gscuser/qzhang/gstat/example_data/fmb.wbroad.csv",
outf="my_output_file.csv",option="protein")
[NOTE]
None

*********************************************************************************

[FUNCTION] mutation_drive_test()
To test if a gene's mutaion affects the overall mutation rate of all other genes 
[USAGE]
-------------------------------------------------------------------------------
mutation_drive_test(inf="input_data_file",outf="output_file_name")
-------------------------------------------------------------------------------
[DATA FORMAT]
A data matrix (or file), multiple columns, tab delimited (sample_id, mutation numbers of gene 1, 
gene 2, ...., gene N)
Example input_data_file "/gscuser/qzhang/gstat/example_data/WU_broad_4mutations.matrix.csv" 
[EXAMPLE RUN]
mutation_drive_test(inf="/gscuser/qzhang/gstat/example_data/WU_broad_4mutations.matrix.csv",
outf="my_output_file_name.csv")
[NOTE]
You can use option alt="less", defult is alt="greater"


#####################
PATHWAY ANALYSIS
#####################

<GSAT module: Group Significance Analysis Test>

[FUNCTION] mutation_pathway_test()
To test if a pathway (or a group of genes) has significant higher mutation rate than others
[USAGE]
----------------------------------------------------------------------------------------
mutation_pathway_test(inf_mut="mutation_file",inf_path="pathway_file",outf="output_file")
----------------------------------------------------------------------------------------
[DATA FORMAT]
Example mutation_file "/gscuser/qzhang/gstat/example_data/mutation_data.csv"
Format: three columns, tab delimited (gene name, total mutation number, total bp length)

Example pathway_file "/gscuser/qzhang/gstat/example_data/gene_path_table_071227.txt"
Format: three (or more) columns, tab delimited (gene ID, gene name, pathway or gene group name 1,pathway or gene group name 2,pathway or gene group name 3 ...)

[EXAMPLE RUN]
mutation_pathway_test(inf_mut="/gscuser/qzhang/gstat/example_data/mutation_data.csv",
inf_path="/gscuser/qzhang/gstat/example_data/gene_path_table_071227.txt",
outf="example_output.csv")

********************************************************************************

[FUNCTION] pathway_test()
To test if a pathway enrichment test
[USAGE]
----------------------------------------------------------------------------------------------------------------------
pathway_test (x,gcolname="gene",lev=c("lev1","lev2","lev3"),yn=c("yn1","yn2","yn3"),cutoff=0.5,outf=NULL,sep="")
----------------------------------------------------------------------------------------------------------------------

####################################
DNA/GENE COPY NUMBER ANALYSIS
####################################

cn.log2ratio(sampleinfo,id=NULL,datadir=NULL,outdir="_log2ratio",sep="",des="tumor/normal pair")

cn.swt(x,wsize=30,wby=1,sd.range=5,chr="all",
chr.col="CHR",pos.col="POS",cn.col="cn",
out.file=NULL,out.rdata=NULL,sep="",draw=F)

cn.gene.test.all(x,out.file=NULL,out.rdata=NULL,cn.lim=4,sep="")

cn.smooth.indv(datadir=NULL,id=NULL,outdir="_smooth.indv")

####################################
GENERALIZED CORRELATION TEST
####################################

cor2test(y,x=NULL,method="cor",cutoff=1,sep="",outf=NULL)

#########################
GENOME VISUALIZATION
#########################

plotgenome(tt, y="p",cutoff=NULL,cutline=2,img=NULL,yscale=NULL,draw=TRUE,
chrom=NULL,mbp=NULL,chr.col="chromosome",pos.col="position",tombp=T)


###########################
TWO SAMPLE TEST 
###########################

<SDAG module: Significantly Difference Among Groups> 

twogrouptest(x,id1,id2,permuN=0)

x: a matrix, rows are samples, columns are varaibles
id1 & id2: row IDs for samples from group 1 & 2
permuN: permutation number, 0 means t test