Last updated: 2018-08-28

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✔ Session information: recorded

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✔ Repository version: 241c630

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Unstaged changes:
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    Modified:   analysis/about.Rmd
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    Modified:   analysis/license.Rmd

Note that any generated files, e.g. HTML, png, CSS, etc., are not included in this status report because it is ok for generated content to have uncommitted changes.

Open IDs

library(haven)

Warning: package 'haven' was built under R version 3.4.4

HTSF_IDs <- read_sav("../data/HTSF_IDs.sav")

library("tidyr")

Warning: package 'tidyr' was built under R version 3.4.4

Obtain HTSF IDs and Baker IDs in the second flowcell run

beginning_baker <- as.data.frame(paste(HTSF_IDs$V2, HTSF_IDs$V1, sep = "-"), stringsAsFactors = FALSE)



adaptor <- sapply(strsplit(HTSF_IDs$V18, split='_', fixed=TRUE), `[`, 5)
s_num <- sapply(strsplit(HTSF_IDs$V18, split='_', fixed=TRUE), `[`, 6)
lane <- sapply(strsplit(HTSF_IDs$V18, split='_', fixed=TRUE), `[`, 7)
pe <- sapply(strsplit(HTSF_IDs$V18, split='_', fixed=TRUE), `[`, 8)
fastq <- sapply(strsplit(HTSF_IDs$V18, split='_', fixed=TRUE), `[`, 9)
check_end <- as.data.frame(paste(adaptor, s_num, lane, pe, fastq, sep = "_"), stringsAsFactors = FALSE)

beginning_baker <- as.data.frame(paste(HTSF_IDs$V2, HTSF_IDs$V1, sep = "-"), stringsAsFactors = FALSE)
end_baker <-  cbind(beginning_baker, check_end)
total_baker <- paste(end_baker[,1],end_baker[,2], sep="_")

HTSF_comb <- as.data.frame(cbind(HTSF_IDs$V18, total_baker, stringsAsFactors = FALSE))

HTSF_comb_170913 <- which(grepl("170913", HTSF_comb[,1]) == TRUE)
HTSF_comb_170913_only <- HTSF_comb[HTSF_comb_170913,]
colnames(HTSF_comb_170913_only) <- cbind("File_1_name", "Beginning_File_2")

write.csv(HTSF_comb_170913_only, "/Users/laurenblake/Dropbox/Lauren Blake/For_Rachel/legend.csv", row.names = FALSE, quote = FALSE)

Put values in order

# Delete the first 24 (RRED study)

ID_name <- as.data.frame(HTSF_IDs$V2[-(1:24)], stringsAsFactors = FALSE)

make_ID <- as.data.frame(unlist(lapply(strsplit(ID_name[,1], split="N"), "[", 2)), stringsAsFactors = FALSE)

non_RED <- as.data.frame((make_ID[,1]), stringsAsFactors = FALSE)
colnames(non_RED) <- c("ID")

# Get non RED individual ID

non_RED_ind <- as.data.frame(substr(non_RED[,1], 2, 5), stringsAsFactors = FALSE)

# Add RED back in

RED <- as.data.frame(HTSF_IDs$V1[(1:24)], stringsAsFactors = FALSE)
colnames(RED) <- c("ID")

# Get RED ID

RED_ind <- as.data.frame(substr(RED[,1], 5, 8), stringsAsFactors = FALSE)

all_id <- rbind(non_RED, RED)

colnames(non_RED_ind) <- c("Individual")
colnames(RED_ind) <- c("Individual")
all_ind <- rbind(non_RED_ind, RED_ind)

# Get time

substrRight <- function(x, n){
  substr(x, nchar(x)-n+1, nchar(x))
}

time_values <- array(NA, dim = c(nrow(all_id),1))

for (i in 1:nrow(all_id)){
  time_values[i,] <- substrRight(all_id[i,], 1)
}

time_values <- as.numeric(time_values)

# Combine ID, individual, and time

info <- cbind(all_id, all_ind, time_values)

# Eliminate duplicates

 all_info <- info[duplicated(info), ]

#write.csv(all_info, "/Users/laurenblake/Dropbox/Lauren Blake/RNA_seq_project/clinical_sample_info.csv", row.names = FALSE, quote = FALSE)

Look at first entry in results from Bioinformatics core

which(grepl("170901_UNC32-K00270_0056_BHLC5LBBXX_AACCGAAC_S19_L002", HTSF_IDs$V18))

[1] 187 188

Session information

sessionInfo()

R version 3.4.3 (2017-11-30)
Platform: x86_64-apple-darwin15.6.0 (64-bit)
Running under: OS X El Capitan 10.11.6

Matrix products: default
BLAS: /Library/Frameworks/R.framework/Versions/3.4/Resources/lib/libRblas.0.dylib
LAPACK: /Library/Frameworks/R.framework/Versions/3.4/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     

other attached packages:
[1] tidyr_0.8.1 haven_1.1.2

loaded via a namespace (and not attached):
 [1] Rcpp_0.12.18      knitr_1.20        whisker_0.3-2    
 [4] magrittr_1.5      workflowr_1.1.1   hms_0.4.2        
 [7] R6_2.2.2          rlang_0.2.2       stringr_1.3.1    
[10] tools_3.4.3       R.oo_1.22.0       git2r_0.23.0     
[13] htmltools_0.3.6   yaml_2.2.0        rprojroot_1.3-2  
[16] digest_0.6.16     tibble_1.4.2      crayon_1.3.4     
[19] purrr_0.2.5       readr_1.1.1       R.utils_2.6.0    
[22] glue_1.3.0        evaluate_0.11     rmarkdown_1.10   
[25] stringi_1.2.4     compiler_3.4.3    pillar_1.3.0     
[28] forcats_0.3.0     backports_1.1.2   R.methodsS3_1.7.1
[31] pkgconfig_2.0.2

This reproducible R Markdown analysis was created with workflowr 1.1.1

Convert_IDs

Lauren Blake

2018-07-11

Open IDs

Obtain HTSF IDs and Baker IDs in the second flowcell run

Put values in order

Look at first entry in results from Bioinformatics core

Session information