correct two typos in the doc

docs/tutorial.rst

@@ -243,15 +243,15 @@ raw files you are using, below is using Thermo Orbitrap::
               '/data/salomonis2/LabFiles/Frank-Li/neoantigen/MS/schuster/MS/OvCa48/OvCa48_classI_Rep#2.raw',
               '/data/salomonis2/LabFiles/Frank-Li/neoantigen/MS/schuster/MS/OvCa48/OvCa48_classI_Rep#3.raw']
     outdir = '/data/salomonis2/LabFiles/Frank-Li/neoantigen/MS/schuster/MS/OvCa48'
-    snaf.proteomics.set_maxquant_configuration(base='mqpar.mxl',dbs=dbs,n_threads=20,inputs=inputs,enzymes=None,enzyme_mode=5,protein_fdr=1,peptide_fdr=0.05,site_fdr=1,
+    snaf.proteomics.set_maxquant_configuration(base='mqpar.xml',dbs=dbs,n_threads=20,inputs=inputs,enzymes=None,enzyme_mode=5,protein_fdr=1,peptide_fdr=0.05,site_fdr=1,
                                                outdir=outdir,minPepLen=8,minPeptideLengthForUnspecificSearch=8,maxPeptideLengthForUnspecificSearch=25)
 
 .. warning::
 
     For the above, even just one file path, please still use list. Second, please use absolute path to avoid maxquant error
 
 
-Above, we need a base 'mqpar.mxl' file to modify upon, we provide a few `base files <https://github.com/frankligy/SNAF/tree/main/maxquant>`_, if your 
+Above, we need a base 'mqpar.xml' file to modify upon, we provide a few `base files <https://github.com/frankligy/SNAF/tree/main/maxquant>`_, if your 
 MS raw files are not in these formats, you can either contact me or just follow the MaxQuant GUI instructions. A automatically generated configuration 
 file (mqpar.xml) will be shown in the outdir that you specified. More information can be found in the :ref:`reference_to_proteomics`.
 

snaf/__init__.py

@@ -17,10 +17,10 @@ def initialize(df,db_dir,gtex_mode='count',software_path=None,binding_method=Non
     :param gtex_mode: string, either 'psi' or 'count'
     :param software_path: string or None, either the path to the netMHCpan4.1 executable or None (using MHCflurry)
     :param binding_method: string or None, either 'netMHCpan' or 'MHCflurry'
-    :param t_min: int, the minimum number of read count the tumor sample should be larget than average number in normal database
+    :param t_min: int, the minimum number of read count the tumor sample should be larger than average number in normal database
     :param n_max: int, the maximum number of average read count normal database count have
-    :param normal_cutoff: int, below which read count we consider a junction is not expressed in normal tissue
-    :param tumor_cutoff: int, above which read count we consider a junction is expressed in tumor tissue
+    :param normal_cutoff: int, below which read count we consider a junction is not expressed in normal tissue, for prevalance mode
+    :param tumor_cutoff: int, above which read count we consider a junction is expressed in tumor tissue, for prevalance mode
     :param normal_prevalance_cutoff: float, if below this fraction, we consider a junction is not present in normal tissue at an appreciable amount
     :param tumor_prevalance_cutoff: float, if above this fraction, we consider a junction is present in tumor tissue at an appreciable amount
     :param add_control: None or a dictionary containing additional controls, additional controls can a dataframe or anndata, for instance, if adding two controls asides from internal GTEx,