Hi everyone,
I am new both to genomic data analysis and R. So my questions may be very basic in nature. Any help will be significant. Thanks in advance ! I have successfully completed QSEA tutorial with given data in MEDIPSData package. However, while using my own data I have few queries.
Similar to example discussed in QSEA package, I am also analyzing MEDIP sequencing data from Tumor (PRAD) and Normal/Control samples. For every tumor and control samples, I have Input Control (IC) alignment bam files. My questions are:
(1) Should I provide IC bam files in the same data frame that have Tumor and Control samples, and do I need to follow specific
nomenclature in group column for IC samples ?
(2) While computing CNV internally from IC, do we need to provide argument "MEDIP = FALSE"? In this case, the addCNV consider fragments with/without CpG dinucleotides ? Is there any resource where addCNV examples with IC have been discussed ? I just want to be sure with the commands I am using to
(3) For TCGA calibration for prostrate cancer, I have downloaded data files TCGA_PRAD_meth450k_level3_wd250.table, TCGA_PRAD_meth450k_level3_wd500.table and TCGA_PRAD_methylation450_level3_beta_values.table from this resource
https://oc-molgen.gnz.mpg.de/owncloud/s/YrQfJnAZLMbTcKb?path=%2F. What processing do I need to perform on these files (.table)
to generate 250/500 bp window size-specific .RData output files that can be directly used by QSEA package functions ?
Best Rakesh
Dear Matthias,
Thank you for the detailed reply to my queries. It is very helpful. As per you suggestion I have prepared my sample table and it looks like this
I will perform both IC and MedIP samples analysis with window size adjustments if required, and post the results here.
Thank you again
Best,
Rakesh
Looks good, this should work.