Update vignette

vignettes/RAIDS.Rmd

@@ -133,7 +133,7 @@ These steps are described in detail in the following.
 
 ### 1.1 Create a directory structure
 
-First, a specific directory structure should be created. The structure must  
+First, a specific directory structure should be created. The structure must 
 correspond to this:
 
 ```
@@ -150,8 +150,8 @@ workingDirectory/
 
 <br>
 
-This following running example creates a temporary working directory structure 
-when the example will be run. 
+This following code creates a temporary working directory structure where the 
+example will be run. 
 
 
 ```{r createDir, echo=TRUE, eval=TRUE, collapse=TRUE, warning=FALSE, message=FALSE}
@@ -306,14 +306,38 @@ data are used to optimize the inference parameters and, with these, the
 ancestry of the input profile donor is inferred.
 
 According to the type of input data (RNA or DNA), a specific function 
-is available.
-
-The *inferAncestry()* function is used for DNA profiles while 
+is available. The *inferAncestry()* function is used for DNA profiles while 
 the *inferAncestryGeneAware()* function is RNA specific.
 
 In this example, the profile is from DNA source and requires the use of the 
 *inferAncestry()* function.
 
+The *inferAncestry()* function requires a specific profile input format. The 
+format is set by the *genoSource* parameter. 
+
+One of those formats is in a VCF format (*genoSource=c("VCF")*). 
+This format follows the VCF standard 
+with at least those genotype fields: _GT_, _AD_ and _DP_. 
+The SNVs  must be germline variants and should include the genotype of the 
+wild-type homozygous at the selected positions in the reference. The VCF file 
+must be gzipped.
+
+A generic SNP file can replace the VCF file (*genoSource=c("generic")*). 
+The format is coma separated and the mandatory columns are:
+
+* _Chromosome_: The name of the chromosome
+* _Position_: The position on the chromosome
+* _Ref_: The reference nucleotide
+* _Alt_: The aternative nucleotide
+* _Count_: The total count
+* _File1R_: The count for the reference nucleotide
+* _File1A_: The count for the alternative nucleotide
+
+Beware that the starting position in the **population reference GDS file** is 
+zero (like BED files). The generic SNP file should also start 
+at position zero.
+
+
 ```{r infere, echo=TRUE, eval=TRUE, collapse=TRUE, warning=FALSE, message=FALSE}
 
 ###########################################################################
@@ -330,7 +354,7 @@ if (requireNamespace("GenomeInfoDb", quietly=TRUE) &&
     chrInfo <- GenomeInfoDb::seqlengths(genome)[1:25]
 
     #######################################################################
-    ## The SNP VCF file of the DNA profile donor
+    ## The demo SNP VCF file of the DNA profile donor
     #######################################################################
     fileDonorVCF <- file.path(dataDir, "example", "snpPileup", "ex1.vcf.gz")