problems on R 4.1.0 on a DELL laptop

[al2na]

Text was 'cut and pasted' from electronic version of book at https://compgenomr.github.io/book/

A small amount of follow up carried out see if there was a simple explanation or work around but no attempt made to go much beyond what someone fairly new to R use might achieve

p182

fit logistic regression model

method and family defines the type of regression

in this case these arguments mean that we are doing logistic

regression

lrFit = train(subtype ~ PDPN,

•            data=training, trControl=trainControl("none"),
  

•            method="glm", family="binomial")
  

Error in eval(predvars, data, env) : object 'PDPN' not found

Strangely while not working with PDPN it worked with other genes e.g CBLN1 and DDX3Y

P209

require(rtracklayer)

session <- browserSession("UCSC",url = 'http://genome-euro.ucsc.edu/cgi-bin/')

genome(session) <- "mm9"

choose CpG island track on chr12

query <- ucscTableQuery(session, track="CpG Islands",table="cpgIslandExt",

•     range=GRangesForUCSCGenome("mm9", "chr12"))
  

Error in GRangesForGenome(genome, chrom = chrom, ranges = ranges, method = "UCSC", :

Failed to obtain information for genome 'mm9'

get the GRanges object for the track

track(query)

Error in h(simpleError(msg, call)) :

error in evaluating the argument 'object' in selecting a method for function 'track': object 'query' not found

P211

library(genomation)

Warning message:

replacing previous import ‘Biostrings::pattern’ by ‘grid::pattern’ when loading ‘genomation’

filePathPeaks=system.file("extdata",

•           "wgEncodeHaibTfbsGm12878Sp1Pcr1xPkRep1.broadPeak.gz",
  

•                   package="compGenomRData")
  

read the peaks from a bed file

pk1.gr=readBroadPeak(filePathPeaks)

Error: No such process

get the peaks that overlap with CpG islands

subsetByOverlaps(pk1.gr,cpgi.gr)

Error in h(simpleError(msg, call)) :

error in evaluating the argument 'x' in selecting a method for function 'subsetByOverlaps': object 'pk1.gr' not found

P217

library(rtracklayer)

File from ENCODE ChIP-seq tracks

bwFile=system.file("extdata","wgEncodeHaibTfbsA549.chr21.bw",package="compGenomRData")

bw.gr=import(bwFile, which=promoter.gr) # get coverage vectors

Error in .local(con, format, text, ...) : UCSC library operation failed

In addition: Warning message:

In .local(con, format, text, ...) : Invalid argument

lseek(3, 844957, invalid 'whence' value (1822621639)) failed

Leading to subsequent errors in rest of section

P225

gene.track <- BiomartGeneRegionTrack(genome = "hg19",

•                                 chromosome = "chr21",
  

•                                 start = 27698681, end = 28083310,
  

•                                 name = "ENSEMBL")
  

Error in gzfile(file, mode) : cannot open the connection

Leading to subsequent errors in rest of section

P239

library(Rqc)

folder = system.file(package="ShortRead", "extdata/E-MTAB-1147")

feeds fastq.qz files in "folder" to quality check function

qcRes=rqc(path = folder, pattern = ".fastq.gz", openBrowser=FALSE)

Error in file(file, ifelse(append, "a", "w")) :

cannot open the connection

In addition: Warning messages:

1: In normalizePath(path.expand(path), winslash, mustWork) :

path[1]="C:\Users\david\AppData\Local\Temp\Rtmpg7tnGG": The system cannot find the file specified

2: In (function (filename = if (onefile) "Rplots.svg" else "Rplot%03d.svg", :

cairo error 'error while writing to output stream'

3: In file(file, ifelse(append, "a", "w")) :

cannot open file 'C:\Users\david\AppData\Local\Temp\Rtmpg7tnGG/rqc_report.md': No such file or directory

rqcCycleQualityBoxPlot(qcRes)

Error in h(simpleError(msg, call)) :

error in evaluating the argument 'x' in selecting a method for function 'perCycleQuality': object 'qcRes' not found

Leading to subsequent errors in rest of section

P243

install.packages("astqcr")

Installing package into 'C:/Users/david/Documents/R/win-library/4.1'

(as 'lib' is unspecified)

Warning: unable to access index for repository https://cran.ma.imperial.ac.uk/src/contrib:

cannot open destfile 'C:\Users\david\AppData\Local\Temp\Rtmpg7tnGG\file1eb47b7e36f1', reason 'No such file or directory'

Warning: unable to access index for repository https://cran.ma.imperial.ac.uk/bin/windows/contrib/4.1:

cannot open destfile 'C:\Users\david\AppData\Local\Temp\Rtmpg7tnGG\file1eb47c802d57', reason 'No such file or directory'

Warning message:

package 'astqcr' is not available for this version of R

p245

write out fastq file with only reads where all

quality scores per base are above 20.

writeFastq(fq[qcount == 0],

•        paste(fastqFile, "Qfiltered", sep="_"))
  

Error: UserArgumentMismatch

P270

plotPCA(countsNormalized[selectedGenes,],

•     col = as.numeric(colData$group), adj = 0.5,
  

•     xlim = c(-0.5, 0.5), ylim = c(-0.5, 0.6))
  

Error in (function (classes, fdef, mtable) :

unable to find an inherited method for function 'plotPCA' for signature '"matrix"'