getCountMatrix

Description

returns the bam data.frame with an additional column counts. Only relevant if the fasta file used for mapping input was previously collapsed via fastx_toolkit to return a fasta read name in the format of readnumber-totalcounts

Usage

getCountMatrix(bam_file,pseudo=FALSE)

Arguments

Value

An object of class data.frame having the values from the original bam file with an additional 'count' column.

Author(s)

Diana H.P. Low

See Also

readBam

Examples

data(ssviz)
getCountMatrix(ctrlbam)

Results

R version 3.3.1 (2016-06-21) -- "Bug in Your Hair"
Copyright (C) 2016 The R Foundation for Statistical Computing
Platform: x86_64-pc-linux-gnu (64-bit)

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Type 'demo()' for some demos, 'help()' for on-line help, or
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> library(ssviz)
Loading required package: Rsamtools
Loading required package: GenomeInfoDb
Loading required package: stats4
Loading required package: BiocGenerics
Loading required package: parallel

Attaching package: 'BiocGenerics'

The following objects are masked from 'package:parallel':

    clusterApply, clusterApplyLB, clusterCall, clusterEvalQ,
    clusterExport, clusterMap, parApply, parCapply, parLapply,
    parLapplyLB, parRapply, parSapply, parSapplyLB

The following objects are masked from 'package:stats':

    IQR, mad, xtabs

The following objects are masked from 'package:base':

    Filter, Find, Map, Position, Reduce, anyDuplicated, append,
    as.data.frame, cbind, colnames, do.call, duplicated, eval, evalq,
    get, grep, grepl, intersect, is.unsorted, lapply, lengths, mapply,
    match, mget, order, paste, pmax, pmax.int, pmin, pmin.int, rank,
    rbind, rownames, sapply, setdiff, sort, table, tapply, union,
    unique, unsplit

Loading required package: S4Vectors

Attaching package: 'S4Vectors'

The following objects are masked from 'package:base':

    colMeans, colSums, expand.grid, rowMeans, rowSums

Loading required package: IRanges
Loading required package: GenomicRanges
Loading required package: Biostrings
Loading required package: XVector
Loading required package: reshape

Attaching package: 'reshape'

The following objects are masked from 'package:S4Vectors':

    expand, rename

Loading required package: ggplot2
Loading required package: RColorBrewer
> png(filename="/home/ddbj/snapshot/RGM3/R_BC/result/ssviz/getCountMatrix.Rd_%03d_medium.png", width=480, height=480)
> ### Name: getCountMatrix
> ### Title: getCountMatrix
> ### Aliases: getCountMatrix
> 
> ### ** Examples
> 
> data(ssviz)
> getCountMatrix(ctrlbam)
DataFrame with 9976 rows and 14 columns
           qname      flag    rname   strand       pos    qwidth      mapq
     <character> <integer> <factor> <factor> <integer> <integer> <integer>
1       74300-21        16     chr1        -   3005526        24        NA
2       95290-16        16     chr1        -   3005696        23        NA
3      114695-13         0     chr1        +   3005832        24        NA
4       97521-15        16     chr1        -   3008048        30        NA
5      100554-15        16     chr1        -   3008818        29        NA
...          ...       ...      ...      ...       ...       ...       ...
9972   111742-13        16     chr1        -  16828975        27        NA
9973    24886-63         0     chr1        +  16833561        27        NA
9974   102926-15        16     chr1        -  16834169        25        NA
9975   122260-12         0     chr1        +  16838393        29        NA
9976   108613-14        16     chr1        -  16838446        26        NA
           cigar     mrnm      mpos     isize                     seq
     <character> <factor> <integer> <integer>          <DNAStringSet>
1            24M       NA         0         0 CATATTGTGC...TCCTTTGTGA
2            23M       NA         0         0 GGTTCTTTCCAGCTTCTGGCTAT
3            24M       NA         0         0 AATTTTCTGA...CCGCCAGACT
4            30M       NA         0         0 TTCCAGTTTT...GCCTTTTGTA
5            29M       NA         0         0 GTTTCACTGT...TAGTTTCTGT
...          ...      ...       ...       ...                     ...
9972         27M       NA         0         0 AAACAACACC...ATAGTCACAA
9973         27M       NA         0         0 TTTGTCTCTG...TTCCATGGGT
9974         25M       NA         0         0 GACTGATTTC...TGGTTGTACA
9975         29M       NA         0         0 TAGGACGTGT...ATTGGCTGCA
9976         26M       NA         0         0 GAGGAAGGCA...ATGGAGTGAA
                        qual    counts
              <PhredQuality> <numeric>
1    IIIIIIIIII...IIIIIIIIII        21
2    IIIIIIIIIIIIIIIIIIIIIII        16
3    IIIIIIIIII...IIIIIIIIII        13
4    IIIIIIIIII...IIIIIIIIII        15
5    IIIIIIIIII...IIIIIIIIII        15
...                      ...       ...
9972 IIIIIIIIII...IIIIIIIIII        13
9973 IIIIIIIIII...IIIIIIIIII        63
9974 IIIIIIIIII...IIIIIIIIII        15
9975 IIIIIIIIII...IIIIIIIIII        12
9976 IIIIIIIIII...IIIIIIIIII        14
> 
> 
> 
> 
> 
> dev.off()
null device 
          1 
>