Update README.md

README.md

@@ -2,9 +2,9 @@ Description
 ===========
 Texomer is a statistical tool designed to perform allele-specific, tumor-deconvoluted transcriptome-exome integration of the bulk whole exome (WES) and whole transcriptome sequencing (WTS) data obtained from autologous patient tissue samples, such as those generated by the cancer cell atlas (TCGA).  It examines the germline SNP and somatic SNV sites in the WES and WTS data and estimates:
 * tumor purity in the bulk DNA and RNA data, respectively  
-* intratumor heterogeneity score in bulk DNA 
-* SNV allele-specific DNA copy number levels in the tumor compartment of the bulk DNA data 
-* SNV allele-specific RNA expression levels in the tumor compartment of the bulk RNA data 
+* intratumor heterogeneity score in bulk DNA
+* SNV allele-specific DNA copy number levels in the tumor compartment of the bulk DNA data
+* SNV allele-specific RNA expression levels in the tumor compartment of the bulk RNA data
 * differential allelic cis-regulatory effect (DACRE) score for each variant allele
 
 If the input includes only the bulk DNA data, Texomer will output only estimates at the DNA level.
@@ -16,7 +16,7 @@ Texomer runs on a x86_64 Linux system, Python 2.7. It depends on samtools and be
 It also requires R (version >= 3.4)
 to run and has dependency on the R packages:
 
-	bbmle, emdbook, copynumber,TitanCNA, facets, mixtools, ASCAT and Sequenza.
+	bbmle, emdbook, copynumber,TitanCNA, facets, mixtools, ASCAT and sequenza.
 
 ***Samtools, bedtools and all R packeages which Texomer depends on are already incorporated in this release. Users do not need to load or install them.***
 
@@ -196,7 +196,7 @@ if you want to run Texomer on only the DNA data:
 **Example 3: Input WES bam files**
 
 	python Texomer.py -p ./ -I BAM -t ./example/Tumor.bam -n ./example/Normal.bam -r ./example/RNA.bam -f ./reference.fa -o ./res3
->The bam file should be aligned based on GRCH38. 
+>The bam file should be aligned based on GRCH38.
 >If you input bam files, Texomer will run longer because it needs to call mutations from the bam files.
 
 
@@ -217,11 +217,11 @@ if you want to run Texomer on only the DNA data:
 
 
 
->- Dmajor: the DNA copy number of the major allele. 
->- Dminor: the DNA copy number of the minor allele. 
->- Rmajor: the RNA expressoin level of the major allele. 
->- Rminor: the RNA expression level of the minor allele. 
->- RTEL: the total RNA expression level of the two alleles. 
+>- Dmajor: the DNA copy number of the major allele.
+>- Dminor: the DNA copy number of the minor allele.
+>- Rmajor: the RNA expressoin level of the major allele.
+>- Rminor: the RNA expression level of the minor allele.
+>- RTEL: the total RNA expression level of the two alleles.
 >- BayesP: the posterior probability that the RNA expression level is discordant with the copy number level
 
 *output.mutations.txt*
@@ -230,19 +230,19 @@ if you want to run Texomer on only the DNA data:
 	chr1	14464	A	T	161	29	Germline	0	0.869112773207088	3	4.26647728279266	0.165069332450197	0.869112773207088	-2.29543007263941	-2.99135865987574
 	chr1	14677	G	A	562	275	Germline	0	0.565025922875357	3	3.23925254542283	0.0153830861293918	0.565025922875357	-2.51927198724942	-2.26822077283764
 
->- refNum: read counts of the reference allele from RNA-seq data. 
->- altNum: read counts of the alernative allele from the RNA-seq data. 
->- type: the types of the mutation are either Germline or Somatic. 
->- altD: the copy number of the alternative allele. 
->- altR: the expression level of the alternative allele. 
->- wildD: the copy number of the reference (wildtype) allele. 
->- wildR: the expression level of the reference (wildtype) allele. 
->- BayesP: the posterior probability that the RNA expression level is discordant with the DNA copy number level. 
->- eASEL: difference between the expression and the copy number levels of the alternative allele (altR-altD) . 
->- AEI: difference between the expression levels of the alternative and the reference alleles (altR-wildR). 
+>- refNum: read counts of the reference allele from RNA-seq data.
+>- altNum: read counts of the alernative allele from the RNA-seq data.
+>- type: the types of the mutation are either Germline or Somatic.
+>- altD: the copy number of the alternative allele.
+>- altR: the expression level of the alternative allele.
+>- wildD: the copy number of the reference (wildtype) allele.
+>- wildR: the expression level of the reference (wildtype) allele.
+>- BayesP: the posterior probability that the RNA expression level is discordant with the DNA copy number level.
+>- eASEL: difference between the expression and the copy number levels of the alternative allele (altR-altD) .
+>- AEI: difference between the expression levels of the alternative and the reference alleles (altR-wildR).
 >- DACRE: the differential allelic cis-regulatory score
 
-Developer 
+Developer
 =========
 Fang Wang ([email protected])