Changes between Version 4 and Version 5 of BIOS_PreparedData


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Timestamp:
Oct 19, 2016 10:45:33 AM (8 years ago)
Author:
rick
Comment:

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  • BIOS_PreparedData

    v4 v5  
    1818Data is stored in R objects, by loading the files in R (e.g. type load('/virdir/Backup/RP3_data/RNASeq/run_01/exoncounts/exon_count_freeze1_R_object.RData') in R) there will be a matrix called RNA in your workspace for the raw data, and RNAs for the TMM normalized data. The row names of these matrices (type rownames(RNAs)) contain gene, exon or transcript IDs, the column names (colnames(RNAs) are the subject BIOS IDs (called uuid in other files). We used
    1919ensembl v.71 for annotation, see [wiki:BIOS_ReferenceFiles Reference and annotation]. If you want to export the data to a tab delimited text file, use write.table(RNAs, file='yourfile.txt', quote =FALSE, col.names=TRUE, row.names=TRUE, sep='\t').[[BR]]
    20 == Freeze II ==
    21 === Data available ===
    22 === Location on VM ===
    23 === How to use the data ===
    24 = DNA methylation data =
    2520
    2621=== Data available ===
    … …  
    7671
    7772Link the files to the RNA-seq, genotype or methylation data by mapping the corresponding IDs.
     73
     74== Freeze II ==
     75=== Data available ===
     76=== Location on VM ===
     77=== How to use the data ===
     78= DNA methylation data =