Merge pull request #76 from mcveanlab/inputExample

update README, add input examples closes #68

README.md

@@ -7,8 +7,9 @@ PfDeconv
 
 _PfDeconv_ is developed as part of the [_Pf3k_](https://www.malariagen.net/projects/parasite/pf3k) project. The _Pf3k_ project is a global collaboration using the latest sequencing technologies to provide a high-resolution view of natural variation in the malaria parasite Plasmodium falciparum. Parasite DNA were extracted from patient blood sample, which often contains more than one parasite strain, with unknown proportions. _PfDeconv_ is used for deconvoluting mixed haplotypes, and reporting the mixture proportions from each sample.
 
-##NEWS
-(to come)
+##METHOD OVERVIEW
+<img src="figures/mixedInfection.png" width="1024">
+
 
 ##INSTALL
 ```bash
@@ -38,14 +39,61 @@ Options              | Useage |
            -rate INT |  MCMC sample rate.
             -noPanel |  Use population level allele frequency as prior.
 
-##Examples :
 
-###Input:
-####Reference allele count
+###Input files:
+Tab-delimited plain text for input. First and second columns record chromosome and position labels respectively. Third columns records the reference allele count, alternative allele count or population level allele frequency.
+
+#### Text file with reference allele count
+```
+CHROM	POS	PG0390.C
+Pf3D7_01_v3	93157	85
+Pf3D7_01_v3	94422	77
+Pf3D7_01_v3	94459	90
+Pf3D7_01_v3	94487	79
+```
+
+#### Text file with alternative allele count
 ```
+CHROM	POS	PG0390.C
+Pf3D7_01_v3	93157	0
+Pf3D7_01_v3	94422	0
+Pf3D7_01_v3	94459	0
+Pf3D7_01_v3	94487	0
 ```
 
+#### Text file with population level alternative allele frequency
+```
+CHROM	POS	PLAF
+Pf3D7_01_v3	93157	0.0190612159917058
+Pf3D7_01_v3	94422	0.135502358766423
+Pf3D7_01_v3	94459	0.156294363760064
+Pf3D7_01_v3	94487	0.143439298925837
+```
+
+#### Reference panel recorded in CSV format
+```
+CHROM,POS,threeD7,dd2gt.from.regression,HB3gt.from.regression,sevenG8gt.from.regression
+Pf3D7_01_v3,93157,0,0,0,1
+Pf3D7_01_v3,94422,0,0,0,1
+Pf3D7_01_v3,94459,0,0,0,1
+Pf3D7_01_v3,94487,0,0,0,1
+```
+
+
+###Input examples :
 ```bash
 ./pfDeconv -ref labStrains/PG0390_first100ref.txt -alt labStrains/PG0390_first100alt.txt -plaf labStrains/labStrains_first100_PLAF.txt -panel labStrains/lab_first100_Panel.txt -o tmp1
 ./pfDeconv -ref labStrains/PG0390_first100ref.txt -alt labStrains/PG0390_first100alt.txt -plaf labStrains/labStrains_first100_PLAF.txt -panel labStrains/lab_first100_Panel.txt -nSample 100 -rate 3
 ```
+
+
+###Output files:
+_PfDeconv_ outputs text files with user-specified prefix:
+
+File Name            | Content |
+:-------------------:| ------------------------------- |
+prefix.log           | Log file records _PfDeconv_ version, input file paths, parameter used and proportion estimates at the final iteration.
+prefix.llk           | Log likelihood of the MCMC chain.
+prefix.prop          | MCMC updates of the proportion estimates.
+prefix.hap           | Haplotypes at the final iteration.
+