Last updated: 2019-04-25

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Knit directory: threeprimeseq/analysis/

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File Version Author Date Message
Rmd 4f1ef74 brimittleman 2019-04-25 add corrrelation

In this analyisis I want to look at the correlation between counts.

library(tidyverse)
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Metadata

metadata=read.table("../data/threePrimeSeqMetaData55Ind_noDup_WASPMAP.txt", header = T, stringsAsFactors = F)
meta_T=metadata %>% filter(grepl("T", Sample_ID)) %>% mutate(samp=paste("X", Sample_ID, sep=""))
meta_N=metadata %>% filter(grepl("N", Sample_ID)) %>%  mutate(samp=paste("X", Sample_ID, sep=""))

Total

totalCounts=read.table("../data/PeakCounts_noMP_genelocanno/filtered_APApeaks_merged_allchrom_refseqGenes.GeneLocAnno_sm_quant_processed_fixed.fc", header = T, stringsAsFactors = F) %>% select(contains("T"),-Geneid, -Chr, -Start, -End, -Strand, -Length,-X19099_T)

totCount_corr= round(cor(totalCounts),2)


meta_TBatch=meta_T %>% select(samp,batch)

target=colnames(totCount_corr)
meta_TBatch$samp <- reorder.factor(meta_TBatch$samp, new.order=target)
meta_TBatch_order=meta_TBatch %>% arrange(samp)


meta_TBatch_order = meta_TBatch_order %>% mutate(color=ifelse(batch=="1", "green", ifelse(batch=="2", "blue", ifelse(batch=="3", "purple", "pink"))))

heatmap.2(as.matrix(totCount_corr),trace="none", dendrogram =c("col"), key=T, ColSideColors=meta_TBatch_order$color)

Nuclear

nucCounts=read.table("../data/PeakCounts_noMP_genelocanno/filtered_APApeaks_merged_allchrom_refseqGenes.GeneLocAnno_sm_quant_processed_fixed.fc", header = T, stringsAsFactors = F) %>% select(contains("N"),-Geneid, -Chr, -Start, -End, -Strand, -Length,-X19099_N)

nucCounts_corr= round(cor(nucCounts),2)


meta_NBatch=meta_N %>% select(samp,batch)

target=colnames(nucCounts_corr)
meta_NBatch$samp <- reorder.factor(meta_NBatch$samp, new.order=target)
meta_NBatch_order=meta_NBatch %>% arrange(samp)


meta_NBatch_order = meta_NBatch_order %>% mutate(color=ifelse(batch=="1", "green", ifelse(batch=="2", "blue", ifelse(batch=="3", "purple", "pink"))))

heatmap.2(as.matrix(nucCounts_corr),trace="none", dendrogram =c("col"), key=T, ColSideColors=meta_NBatch_order$color)



sessionInfo()
R version 3.5.1 (2018-07-02)
Platform: x86_64-apple-darwin15.6.0 (64-bit)
Running under: macOS  10.14.1

Matrix products: default
BLAS: /Library/Frameworks/R.framework/Versions/3.5/Resources/lib/libRblas.0.dylib
LAPACK: /Library/Frameworks/R.framework/Versions/3.5/Resources/lib/libRlapack.dylib

locale:
[1] en_US.UTF-8/en_US.UTF-8/en_US.UTF-8/C/en_US.UTF-8/en_US.UTF-8

attached base packages:
[1] stats     graphics  grDevices utils     datasets  methods   base     

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[13] tidyverse_1.2.1

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[28] backports_1.1.3    jsonlite_1.6       fs_1.2.6          
[31] hms_0.4.2          digest_0.6.18      stringi_1.3.1     
[34] grid_3.5.1         rprojroot_1.3-2    bitops_1.0-6      
[37] cli_1.0.1          tools_3.5.1        magrittr_1.5      
[40] lazyeval_0.2.1     crayon_1.3.4       whisker_0.3-2     
[43] pkgconfig_2.0.2    xml2_1.2.0         lubridate_1.7.4   
[46] assertthat_0.2.0   rmarkdown_1.11     httr_1.4.0        
[49] rstudioapi_0.9.0   R6_2.4.0           nlme_3.1-137      
[52] git2r_0.24.0       compiler_3.5.1