Upgrading to R 3.2.0 on Windows

If you are using Windows you can easily upgrade to the latest version of R using the installr package. Simply run the following code:

# installing/loading the latest installr package:
install.packages("installr"); library(installr) #load / install+load installr
 
updateR() # updating R.

Running “updateR()” will detect if there is a new R version available, and if so it will download+install it (etc.).

If you are an R blogger yourself you are invited to add your own R content feed to this site (Non-English R bloggers should add themselves- here)

NEW FEATURES

• anyNA() gains a recursive argument.
• When x is missing and names is not false (including the default value), Sys.getenv(x, names) returns an object of class "Dlist" and hence prints tidily.
• (Windows.) shell() no longer consults the environment variable SHELL: too many systems have been encountered where it was set incorrectly (usually to a path where software was compiled, not where it was installed). R_SHELL, the preferred way to select a non-default shell, can be used instead.
• Some unusual arguments to embedFonts() can now be specified as character vectors, and the defaults have been changed accordingly.
• Functions in the Summary group duplicate less. (PR#15798)
• (Unix-alikes.) system(cmd, input = ) now uses ‘shell-execution-environment’ redirection, which will be more natural if cmd is not a single command (but requires a POSIX-compliant shell). (Wish of PR#15508)
• read.fwf() and read.DIF() gain a fileEncoding argument, for convenience.
• Graphics devices can add attributes to their description in .Device and .Devices. Several of those included with R use a "filepath" attribute.
• pmatch() uses hashing in more cases and so is faster at the expense of using more memory. (PR#15697)
• pairs() gains new arguments to select sets of variables to be plotted against each other.
• file.info(, extra_cols = FALSE) allows a minimal set of columns to be computed on Unix-alikes: on some systems without properly-configured caching this can be significantly faster with large file lists.
• New function dir.exists() in package base to test efficiently whether one or more paths exist and are directories.
• dput() and friends gain new controls hexNumeric and digits17 which output double and complex quantities as, respectively, binary fractions (exactly, see sprintf("%a")) and as decimals with up to 17 significant digits.
• save(), saveRDS() and serialize() now support ascii = NA which writes ASCII files using sprintf("%a") for double/complex quantities. This is read-compatible with ascii = TRUE but avoids binary->decimal->binary conversions with potential loss of precision. Unfortunately the Windows C runtime’s lack of C99 compliance means that the format cannot be read correctly there in R before 3.1.2.
• The default for formatC(decimal.mark =) has been changed to be getOption("OutDec"); this makes it more consistent with format() and suitable for use in print methods, e.g. those for classes "density", "ecdf", "stepfun" and "summary.lm".

  getOption("OutDec") is now consulted by the print method for class "kmeans", by cut(), dendrogram(), plot.ts() and quantile() when constructing labels and for the report fromlegend(trace = TRUE).

  (In part, wish of PR#15819.)

• printNum() and hence format() and formatC() give a warning if big.mark and decimal.mark are set to the same value (period and comma are not uncommonly used for each, and this is a check that conventions have not got mixed).
• merge() can create a result which uses long vectors on 64-bit platforms.
• dget() gains a new argument keep.source which defaults to FALSE for speed (dput() and dget() are most often used for data objects where this can make dget() many times faster).
• Packages may now use a file of common macro definitions in their help files, and may import definitions from other packages.
• A number of macros have been added in the new ‘share/Rd’ directory for use in package overview help pages, and promptPackage() now makes use of them.
• tools::parse_Rd() gains a new permissive argument which converts unrecognized macros into text. This is used by utils:::format.bibentry to allow LaTeX markup to be ignored.
• options(OutDec =) can now specify a multi-byte character, e.g., options(OutDec = "u00b7") in a UTF-8 locale.
• is.recursive(x) is no longer true when x is an external pointer, a weak reference or byte code; the first enables all.equal(x, x) when x .
• ls() (aka objects()) and as.list.environment() gain a new argument sorted.
• The "source" attribute (which has not been added to functions by R since before R version 2.14.0) is no longer treated as special.
• Function returnValue() has been added to give on.exit() code access to a function’s return value for debugging purposes.
• crossprod(x, y) allows more matrix coercions when x or y are vectors, now equalling t(x) %*% y in these cases (also reported by Radford Neal). Similarly, tcrossprod(x,y) and %*% work in more cases with vector arguments.
• Utility function dynGet() useful for detecting cycles, aka infinite recursions.
• The byte-code compiler and interpreter include new instructions that allow many scalar subsetting and assignment and scalar arithmetic operations to be handled more efficiently. This can result in significant performance improvements in scalar numerical code.
• apply(m, 2, identity) is now the same as the matrix m when it has named row names.
• A new function debuggingState() has been added, allowing to temporarily turn off debugging.
• example() gets a new optional argument run.donttest and tools::Rd2ex() a corresponding commentDonttest, with a default such that example(..) in help examples will run donttest code only if used interactively (a change in behaviour).
• rbind.data.frame() gains an optional argument make.row.names, for potential speedup.
• New function extSoftVersion() to report on the versions of third-party software in use in this session. Currently reports versions of zlib, bzlib, the liblzma from xz, PCRE, ICU, TRE and the iconv implementation.

  A similar function grSoftVersion() in package grDevices reports on third-party graphics software.

  Function tcltk::tclVersion() reports the Tcl/Tk version.

• Calling callGeneric() without arguments now works with primitive generics to some extent.
• vapply(x, FUN, FUN.VALUE) is more efficient notably for large length(FUN.VALUE); as extension of PR#16061.
• as.table() now allows tables with one or more dimensions of length 0 (such as as.table(integer())).
• names(x) now clears the names of call and ... objects.
• library() will report a warning when an insufficient dependency version is masking a sufficient one later on the library search path.
• A new plot() method for class "raster" has been added.
• New check_packages_in_dir_changes() function in package tools for conveniently analyzing how changing sources impacts the check results of their reverse dependencies.
• Speed-up from Peter Haverty for ls() and methods:::.requirePackage() speeding up package loading. (PR#16133)
• New get0() function, combining exists() and get() in one call, for efficiency.
• match.call() gains an envir argument for specifying the environment from which to retrieve the ... in the call, if any; this environment was wrong (or at least undesirable) when thedefinition argument was a function.
• topenv() has been made .Internal() for speedup, based on Peter Haverty’s proposal in PR#16140.
• getOption() no longer calls options() in the main case.
• Optional use of libcurl (version 7.28.0 from Oct 2012 or later) for Internet access:
  • capabilities("libcurl") reports if this is available.
  • libcurlVersion() reports the version in use, and other details of the "libcurl" build including which URL schemes it supports.
  • curlGetHeaders() retrieves the headers for http://, https://, ftp:// and ftps:// URLs: analysis of these headers can provide insights into the ‘existence’ of a URL (it might for example be permanently redirected) and is so used in R CMD check --as-cran.
  • download.file() has a new optional method "libcurl" which will handle more URL schemes, follow redirections, and allows simultaneous downloads of multiple URLs.
  • url() has a new method "libcurl" which handles more URL schemes and follows redirections. The default method is controlled by a new option url.method, which applies also to the opening of URLs via file() (which happens implicitly in functions such as read.table.)
  • When file() or url() is invoked with a https:// or ftps:// URL which the current method cannot handle, it switches to a suitable method if one is available.
• (Windows.) The DLLs ‘internet.dll’ and ‘internet2.dll’ have been merged. In this version it is safe to switch (repeatedly) between the internal and Windows internet functions within an Rsession.

  The Windows internet functions are still selected by flag –internet2 or setInternet2(). This can be overridden for an url() connection via its new method argument.

  download.file() has new method "wininet", selected as the default by –internet2 or setInternet2().

• parent.env<- can no longer modify the parent of a locked namespace or namespace imports environment. Contributed by Karl Millar.
• New function isLoadedNamespace() for readability and speed.
• names(env) now returns all the object names of an environment env, equivalently to ls(env, all.names = TRUE, sorted = FALSE) and also to the names of the corresponding list,names(as.list(env, all.names = TRUE)). Note that although names() returns a character vector, the names have no particular ordering.
• The memory manager now grows the heap more aggressively. This reduces the number of garbage collections, in particular while data or code are loaded, at the expense of slightly increasing the memory footprint.
• New function trimws() for removing leading/trailing whitespace.
• cbind() and rbind() now consider S4 inheritance during S3 dispatch and also obey deparse.level.
• cbind() and rbind() will delegate recursively to methods::cbind2 (methods::rbind2) when at least one argument is an S4 object and S3 dispatch fails (due to ambiguity).
• (Windows.) download.file(quiet = FALSE) now uses text rather than Windows progress bars in non-interactive use.
• New function hsearch_db() in package utils for building and retrieving the help search database used by help.search(), along with functions for inspecting the concepts and keywords in the help search database.
• New function .getNamespaceInfo(), a no-check version of getNamespaceInfo() mostly for internal speedups.
• The help search system now takes keyword entries in Rd files which are not standard keywords (as given in ‘KEYWORDS’ in the R documentation directory) as concepts. For standard keyword entries the corresponding descriptions are additionally taken as concepts.
• New lengths() function for getting the lengths of all elements in a list.
• New function toTitleCase() in package tools, tailored to package titles.
• The matrix methods of cbind() and rbind() allow matrices as inputs which have 2^31 or more elements. (For cbind(), wish of PR#16198.)
• The default method of image() has an explicit check for a numeric or logical matrix (which was always required).
• URLencode() will not by default encode further URLs which appear to be already encoded.
• BIC(mod) and BIC(mod, mod2) now give non-NA numbers for arima() fitted models, as nobs(mod) now gives the number of “used” observations for such models. This fixes PR#16198, quite differently than proposed there.
• The print() methods for "htest", "pairwise.htest" and "power.htest" objects now have a digits argument defaulting to (a function of) getOption("digits"), and influencing all printed numbers coherently. Unavoidably, this changes the display of such test results in some cases.
• Code completion for namespaces now recognizes all loaded namespaces, rather than only the ones that are also attached.
• The code completion mechanism can now be replaced by a user-specified completer function, for (temporary) situations where the usual code completion is inappropriate.
• unzip() will now warn if it is able to detect truncation when unpacking a file of 4GB or more (related to PR#16243).
• methods() reports S4 in addition to S3 methods; output is simplified when the class argument is used. .S3methods() and methods::.S4methods() report S3 and S4 methods separately.
• Higher order functions such as the apply functions and Reduce() now force arguments to the functions they apply in order to eliminate undesirable interactions between lazy evaluation and variable capture in closures. This resolves PR#16093.

More at http://cran.rstudio.com/

Reference: http://www.r-bloggers.com/r-3-2-0-is-released-using-the-installr-package-to-upgrade-in-windows-os/

Main research topics:
- Comparative and Population Genomics of Plant Symbionts
- Parasite Genome Evolution
- Experimental Evolution of Microbial Symbionts and Parasites
- Phylogenomics of Early Branching Fungi

More at http://corradilab.weebly.com/

Bioinformatics Textbook Track

Find more about Rosalind puzzle at http://rosalind.info/problems/list-view/?location=bioinformatics-textbook-track

I will provide solution of all the Rosalind problem with Perl for community.

Check out the right sidebar for more links ...

More at http://catchenlab.life.illinois.edu/stacks/

Address of the bookmark: http://catchenlab.life.illinois.edu/stacks/

More at https://bitbucket.org/henryhzhang/rcircos/src

Address of the bookmark: https://bitbucket.org/henryhzhang/rcircos/src

Address of the bookmark: https://github.com/al2na/methylKit

Address of the bookmark: http://4dgenome.research.chop.edu/

Paper:http://www.ncbi.nlm.nih.gov/pubmed/25940625

More at http://cbio.ensmp.fr/centurion/

Address of the bookmark: http://cbio.ensmp.fr/centurion/

Address of the bookmark: http://biobits.org/samtools_primer.html

bcftools: a set of companion tools, currently bundled with SAMtools, for identifying and filtering genomics variants.

bowtie: widely used, open source alignment software for aligning raw sequence reads to a reference genome.

BAM Format: binary, compressed format for storing SAM data.

BCF Format: Binary call format. Binary, compressed format for storing VCF data.

CIGAR String: Compact Idiosyncratic Gapped Alignment Report. A compact string that (partially) summarizes the alignment of a raw sequence read to the reference genome. Three core abbreviations are used: M for alignment match; I for insertion; and D for Deletion. For example, a CIGAR string of 5M2I63M indicates that the first 5 base pairs of the read align to the reference, followed by 2 base pairs, which are unique to the read, and not in the reference genome, followed by an additional 63 base pairs of alignment.

FASTA Format: text format for storing raw sequence data. For example, the FASTA file at: http://www.ncbi.nlm.nih.gov/nuccore/NC_008253 contains entire genome for Escherichia coli 536.

FASTQ Format: text format for storing raw sequence data along with quality scores for each base; usually generated by sequencing machines.

genotype likelihood: the probability that a specific genotype is present in the sample of interest. Genotype likelihoods are usually expressed as a Phred-scaled probability, where P = 10 ^ (-Q/10). For example, if the genotype TT (both alleles are T) at position 1,299,132 in human chromosome 12 (reference G) is 37, this translates to a probability of 10^-37/10 = 0.0001995, meaning that there is very low probability that the reads in your sample support a TT genotype. On the other hand, a genotype of AA at the same position with a score of 0 translates into a probability of 10^-0 = 1, indicating extremely high probability that your sample contains a homozygous mutation of G to A.

mate-pair: in paired-end sequencing, both ends of a single DNA or RNA fragment are sequenced, but the intermediate region is not. The two ends which are sequenced form a pair, and are frequently referred to as mate-pairs.

QNAME: unique identifier of a raw sequence read (also known as the Query Name). Used in FASTQ and SAM files.

paired-end sequencing: sequencing process where both ends of a single DNA or RNA fragment are sequenced, but the intermediate region is not. Particularly useful for identifying structural rearrangements, including gene fusions.

Phred-scaled probability: a scaled value (Q) used to compactly summarize a probability, where P = 10^-Q/10. For example, a Phred Q score of 10 translates to probability (P) = 10^-10/10 = 0.1. Phred-scaled probabilities are common in next-generation sequencing, and are used to represent multiple types of quality metrics, including quality of base calls, quality of mappings, and probabilities associated with specific genotypes. The name Phred refers to the original Phred base-calling software, which first used and developed the scale.

Phred quality score: a score assigned to each base within a sequence, quantifying the probability that the base was called incorrectly. Scores use a Phred-scaled probability metric. For example, a Phred Q score of 10 translates to P=10^-10/10 = 0.1, indicating that the base has a 0.1 probability of being incorrect. Higher Phred score correspond to higher accuracy. In the FASTQ format, Phred scores are represented as single ASCII letters. For details on translating between Phred scores and ASCII values, refer to Table 1 of this useful blog post from Damian Gregory Allis.

read-length: the number of base pairs that are sequenced in an individual sequence read.

read-depth: the number of sequence reads that pile up at the same genomic location. For example, 30X read-depth coverage indicates that the genomic location is covered by 30 independent sequencing reads. Increased read-depth translates into higher confidence for calling genomic variants.

RNAME: reference genome identifier (also known as the Reference Name). Within a SAM formatted file, the RNAME identifies the reference genome where the raw read aligns.

SAM Flag: a single integer value (e.g. 16), which encodes multiple elements of meta-data regarding a read and its alignment. Elements include: whether the read is one part of a paired-end read, whether the read aligns to the genome, and whether the read aligns to the forward or reverse strand of the genome. A useful online utility decodes a single SAM flag value into plain English.

SAM Format: Text file format for storing sequence alignments against a reference genome. See also BAM Format.

SAMtools: widely used, open source command line tool for manipulating SAM/BAM files. Includes options for converting, sorting, indexing and viewing SAM/BAM files. The SAMtools distribution also includes bcftools, a set of command line tools for identifying and filtering genomics variants. Created by Heng Li, currently of the Broad Institute.

single-read sequencing: sequencing process where only one end of a DNA or RNA fragment is sequenced. Contrast with paired-end sequencing.

VCF Format: Variant call format. Text file format for storing genomic variants, including single nucleotide polymorphisms, insertions, deletions and structural rearrangements. See also BCF format.

NextGenerationSequencing
A high-throughput sequencing method which parallelizes the sequencing process, producing thousands or millions of sequences at once.

DeepSequencing
Techniques of nucleotide sequence analysis that increase the range, complexity, sensitivity, and accuracy of results by greatly increasing the scale of operations and thus the number of nucleotides, and the number of copies of each nucleotide sequenced.

Paired-EndSequencing
Sequence both ends of the same fragment and keep track of the paired data.

Adapter
Short oligonucleotides which are attached to the DNA to be sequenced. An adapter can provide a priming site for both amplification and sequencing of the adjoining, unknown nucleic acid.

Library
A collection of DNA fragments with adapters ligated to each end.

BridgeAmplification
Generation of in situ copies of a specific DNA molecule on an oligo-decorated solid support.

EmulsionPCR
A method for bead-based amplification of a library. A single adapter-bound fragment is attached to the surface of a bead, and an oil emulsion containing necessary amplification reagents is formed around the bead/fragment component. Parallel amplification of millions of beads with millions of single strand fragments produces a sequencer-ready library.

Alignment
Mapping of sequence reads to a known reference sequence

Referencesequence/genome 
A fully assembled version of a genome that can be used for mapping short DNA sequence reads for comparisons of genomes from various individuals

CoverageDepth
The number of nucleotides from reads that are mapped to a given position of reference genome.

Specificity 
The percentage of sequences that map to the intended targets out of total bases per run.

Uniformity 
The variability in sequence coverage across target regions.

Homopolymer
Uninterrupted stretch of a single nucleotide type (e.g., TTT or GGGGGG)

InDel
InDel stands for Insertion or deletion. A form of structural variation in which a DNA segment is either deleted or inserted.

SNP 

SNP stands for Single Nucleotide Polymorphism. A single base difference found when comparing the same DNA sequence from two different individuals.