Last data update: 2014.03.03
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R: Output count/weight summary by sequences
summarizeBySeq | R Documentation |
Output count/weight summary by sequences
Description
Output count/weight summary by sequences with each row representing each sequences
Usage
summarizeBySeq(assignedSeqs, by =c("Weight", "SEQid"))
Arguments
assignedSeqs |
output from assignSeq2REsite
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by |
Weight if sum up the weight for each sequence, SEQid if sum the occurrence of each sequence
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Value
a matrix with SEQid as the first column and total count/weight as the second column
Author(s)
Lihua Julie Zhu
See Also
summarizeByRE, assignSeq2REsite
Examples
library(REDseq)
data(example.assignedREDseq)
summarizeBySeq(example.assignedREDseq, by="Weight")
summarizeBySeq(example.assignedREDseq,by="SEQid")
Results
R version 3.3.1 (2016-06-21) -- "Bug in Your Hair"
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Platform: x86_64-pc-linux-gnu (64-bit)
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> library(REDseq)
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: BSgenome.Celegans.UCSC.ce2
Loading required package: BSgenome
Loading required package: S4Vectors
Loading required package: stats4
Attaching package: 'S4Vectors'
The following objects are masked from 'package:base':
colMeans, colSums, expand.grid, rowMeans, rowSums
Loading required package: IRanges
Loading required package: GenomeInfoDb
Loading required package: GenomicRanges
Loading required package: Biostrings
Loading required package: XVector
Loading required package: rtracklayer
Loading required package: multtest
Loading required package: Biobase
Welcome to Bioconductor
Vignettes contain introductory material; view with
'browseVignettes()'. To cite Bioconductor, see
'citation("Biobase")', and for packages 'citation("pkgname")'.
Loading required package: ChIPpeakAnno
Loading required package: grid
Loading required package: VennDiagram
Loading required package: futile.logger
No methods found in "IRanges" for requests: %in%
> png(filename="/home/ddbj/snapshot/RGM3/R_BC/result/REDseq/summarizeBySeq.Rd_%03d_medium.png", width=480, height=480)
> ### Name: summarizeBySeq
> ### Title: Output count/weight summary by sequences
> ### Aliases: summarizeBySeq
> ### Keywords: misc
>
> ### ** Examples
>
> library(REDseq)
> data(example.assignedREDseq)
> summarizeBySeq(example.assignedREDseq, by="Weight")
SEQid total.weight
00000036 "00000036" "1"
00000037 "00000037" "1"
00000038 "00000038" "1"
00000039 "00000039" "1"
00000040 "00000040" "1"
00000041 "00000041" "1"
00000052 "00000052" "1"
00000053 "00000053" "1"
00000054 "00000054" "1"
00000055 "00000055" "1"
00000056 "00000056" "1"
00000057 "00000057" "1"
00000058 "00000058" "1"
00000059 "00000059" "1"
00000060 "00000060" "1"
00000061 "00000061" "1"
00000065 "00000065" "1"
00000066 "00000066" "1"
00000067 "00000067" "1"
00000068 "00000068" "1"
00000070 "00000070" "1"
00000071 "00000071" "1"
00000072 "00000072" "1"
00000073 "00000073" "1"
00000074 "00000074" "1"
00000075 "00000075" "1"
00000076 "00000076" "1"
00000077 "00000077" "1"
00000078 "00000078" "1"
00000079 "00000079" "1"
00000080 "00000080" "1"
00000081 "00000081" "1"
00000084 "00000084" "1"
> summarizeBySeq(example.assignedREDseq,by="SEQid")
SEQid total.count
1 00000036 1
2 00000037 1
3 00000038 1
4 00000039 1
5 00000040 1
6 00000041 2
7 00000052 1
8 00000053 2
9 00000054 1
10 00000055 1
11 00000056 1
12 00000057 1
13 00000058 1
14 00000059 1
15 00000060 1
16 00000061 1
17 00000065 1
18 00000066 1
19 00000067 1
20 00000068 1
21 00000070 2
22 00000071 2
23 00000072 1
24 00000073 1
25 00000074 1
26 00000075 1
27 00000076 1
28 00000077 4
29 00000078 4
30 00000079 1
31 00000080 1
32 00000081 2
33 00000084 1
>
>
>
>
>
> dev.off()
null device
1
>
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