Update workflow.md

Docs/workflow.md

@@ -29,7 +29,7 @@ The latter works for the focally amplified regions with amplified baseline. This
 After this, the identified amplicons were merged together if the two adjacent amplicons are 1) close enough (less than 3 Mb away to each other) AND 2) the copy number of the intervening segment is clearly amplified from the baseline (2X of baseline copy number or greater AND copy number of 4 or greater). Amplicons were also filtered out if they are only moderately amplified from the adjacent segments (copy number difference less then 3). This pattern was often observed in the chromosomal regions with frequent nested or overlapped tandem duplications. Last, considering the known mechanistic relationship between the focal amplifications and chromothripsis, we expanded the amplified region boundaries if the boundary is close enough (within 1 Mb) to the copy number junction where the copy number of the adjacent segment is at the baseline copy number of given chromosome arm or less. Then SVs are associated with the boundaries of amplicons based on their physical proximity.
 
 ## Association with epigenomics data
-The following functions can be loaded by running `**association.with.epigenomics.data.R**` under `**focal-amplification/R**` folder. The relavant data files are found in under `**focal-amplification/Data**` folder. The nessary input files for the functions are typically set as default.
+The following functions can be loaded by running **association.with.epigenomics.data.R** under **focal-amplification/R** folder. The relavant data files are found in under **focal-amplification/Data** folder. The nessary input files for the functions are typically set as default.
 
 To determine which epigenomic features were associated with the initial SV events of the amplicons in breast cancers, we integrated the SVs at the amplicon boundaries with various chromatin features. This function `association.with.chromatin.features` takes the coordinates of bindings for each factor and boundary positions in 100-kb bins as inputs and computs the enrichment p-values of the factor by Fisher's exact test.
 
@@ -38,7 +38,7 @@ The function `comparison.er.e2.control`compares the distributions of ERa binding
 To see the association between the recurrence of amplicon boundaries and ERa intensity in E2-treated cells, we calculated the recurrence of patinets and accumulated ERa binding intensity of ERa in E2-treated MCF7 cells in 100-kb bins. This function `association.recurrence.e2.er.intensity` takes the information of the recurrence and ERa intensity and displays the increase of ERa binding intensity at the binns with a high recurrence.
 
 ## Association with 3D chromatin interaction data
-The following functions can be loaded by running `association.with.epigenomics.data.R` under `focal-amplification/R` folder. The relavant data files are found in under `focal-amplification/Data` folder. The nessary input files for the functions are typically set as default.
+The following functions can be loaded by running **association.with.epigenomics.data.R** under **focal-amplification/R** folder. The relavant data files are found in under **focal-amplification/Data** folder. The nessary input files for the functions are typically set as default.
 
 To analyze the association between amplicon boundaries and chromatin proximity, we obtained Hi-C data from T47D luminal breast cancer cell line which doesn't have major translocation major between the chromosomes of our interests such as between chromosomes 8, 11 and 17 and used contact frequencies normalized by balance-based method (KR normalization). The function `association.recurrence.3d.contact.t47d` takes SVs from the amplicon boundareis and the location of the folder containing of contact frequeincy information in 2.5Mb as inputs and displays the association between them.