R adding slots to existing S4 object - r

I am trying to follow this answer but getting lost with what to change for my example. Please can someone spell out specifically for the below?
I have the following S4 object called "classic":
> str(classic)
Formal class 'topGOresult' [package "topGO"] with 5 slots
..# description: chr "Custom Afol today"
..# score : Named num [1:7633] 0.5735 0.0883 0.8081 0.8005 0.4941 ...
.. ..- attr(*, "names")= chr [1:7633] "GO:0000002" "GO:0000003" "GO:0000018" "GO:0000027" ...
..# testName : chr "fisher"
..# algorithm : chr "classic"
.. ..- attr(*, "testClass")= chr "classicCount"
..# geneData : Named int [1:4] 9171 620 5 5361
.. ..- attr(*, "names")= chr [1:4] "Annotated" "Significant" "NodeSize" "SigTerms"
I am able to edit contents of existing slots, such as:
classic#description = "Custom Afol today"
However, I would like to add a new slot called "ontology" with character input of "BP". Is there a way to add a new slot to an existing object such as this?
Many thanks in advance for help.

Related

How to convert dataframe (or vector) to matrix to use R baseline package for data other than the sample data provided?

I have data in the form of a dataframe of x and y values that when plotted looks like this:
(The portion highlighted in green corresponds to the dput() data below).
I want to use the baseline package to experiment with the different baseline correction algorithms described in "Liland, K. H., Almøy, T., & Mevik, B.-H. (2010). Optimal Choice of Baseline Correction for Multivariate Calibration of Spectra. Applied Spectroscopy, 64(9), 1007–1016. doi:10.1366/000370210792434350".
The package specifies that "data must be organized as row vectors in a matrix or data.frame", however, simply converting my y values to a matrix doesn't work:
> baseline(as.matrix(y, byrow=T))
Error in rep(3, p - 4) : invalid 'times' argument
The example data that is provided with the package has a structure that I can't interpret or figure out how to emulate with my own data.
> library(baseline)
> data(milk)
> str(milk)
'data.frame': 45 obs. of 2 variables:
$ cow : num 0 0.25 0.375 0.875 0.5 0.75 0.5 0.125 0 0.125 ...
$ spectra: num [1:45, 1:21451] 1029 371 606 368 554 ...
..- attr(*, "dimnames")=List of 2
.. ..$ : NULL
.. ..$ : chr [1:21451] "4999.94078628963" "5001.55954267662" "5003.17856106153" "5004.79784144435" ...
- attr(*, "terms")=Classes 'terms', 'formula' language cow ~ spectra
.. ..- attr(*, "variables")= language list(cow, spectra)
.. ..- attr(*, "factors")= int [1:2, 1] 0 1
.. .. ..- attr(*, "dimnames")=List of 2
.. .. .. ..$ : chr [1:2] "cow" "spectra"
.. .. .. ..$ : chr "spectra"
.. ..- attr(*, "term.labels")= chr "spectra"
.. ..- attr(*, "order")= int 1
.. ..- attr(*, "intercept")= int 1
.. ..- attr(*, "response")= int 1
.. ..- attr(*, ".Environment")=<environment: R_GlobalEnv>
.. ..- attr(*, "predvars")= language list(cow, spectra)
.. ..- attr(*, "dataClasses")= Named chr [1:2] "numeric" "nmatrix.21451"
.. .. ..- attr(*, "names")= chr [1:2] "cow" "spectra"
If anyone can tell me how I can call baseline() on my own data, I would greatly appreciate it.
Here is a subsection of the data I'm working with, corresponding to the green highlighted portion of the plot above:
> dput(fid_df[fid_df$rt>12.5&fid_df$rt<12.8,])
structure(list(rt = c(12.5002866914485, 12.5011200182712, 12.5019533450939,
12.5027866719166, 12.5036199987393, 12.5044533255619, 12.5052866523846,
12.5061199792073, 12.50695330603, 12.5077866328527, 12.5086199596754,
12.5094532864981, 12.5102866133207, 12.5111199401434, 12.5119532669661,
12.5127865937888, 12.5136199206115, 12.5144532474342, 12.5152865742568,
12.5161199010795, 12.5169532279022, 12.5177865547249, 12.5186198815476,
12.5194532083703, 12.5202865351929, 12.5211198620156, 12.5219531888383,
12.522786515661, 12.5236198424837, 12.5244531693064, 12.5252864961291,
12.5261198229517, 12.5269531497744, 12.5277864765971, 12.5286198034198,
12.5294531302425, 12.5302864570652, 12.5311197838878, 12.5319531107105,
12.5327864375332, 12.5336197643559, 12.5344530911786, 12.5352864180013,
12.536119744824, 12.5369530716466, 12.5377863984693, 12.538619725292,
12.5394530521147, 12.5402863789374, 12.5411197057601, 12.5419530325827,
12.5427863594054, 12.5436196862281, 12.5444530130508, 12.5452863398735,
12.5461196666962, 12.5469529935189, 12.5477863203415, 12.5486196471642,
12.5494529739869, 12.5502863008096, 12.5511196276323, 12.551952954455,
12.5527862812776, 12.5536196081003, 12.554452934923, 12.5552862617457,
12.5561195885684, 12.5569529153911, 12.5577862422138, 12.5586195690364,
12.5594528958591, 12.5602862226818, 12.5611195495045, 12.5619528763272,
12.5627862031499, 12.5636195299725, 12.5644528567952, 12.5652861836179,
12.5661195104406, 12.5669528372633, 12.567786164086, 12.5686194909087,
12.5694528177313, 12.570286144554, 12.5711194713767, 12.5719527981994,
12.5727861250221, 12.5736194518448, 12.5744527786674, 12.5752861054901,
12.5761194323128, 12.5769527591355, 12.5777860859582, 12.5786194127809,
12.5794527396035, 12.5802860664262, 12.5811193932489, 12.5819527200716,
12.5827860468943, 12.583619373717, 12.5844527005397, 12.5852860273623,
12.586119354185, 12.5869526810077, 12.5877860078304, 12.5886193346531,
12.5894526614758, 12.5902859882984, 12.5911193151211, 12.5919526419438,
12.5927859687665, 12.5936192955892, 12.5944526224119, 12.5952859492346,
12.5961192760572, 12.5969526028799, 12.5977859297026, 12.5986192565253,
12.599452583348, 12.6002859101707, 12.6011192369933, 12.601952563816,
12.6027858906387, 12.6036192174614, 12.6044525442841, 12.6052858711068,
12.6061191979295, 12.6069525247521, 12.6077858515748, 12.6086191783975,
12.6094525052202, 12.6102858320429, 12.6111191588656, 12.6119524856882,
12.6127858125109, 12.6136191393336, 12.6144524661563, 12.615285792979,
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12.6227857343831, 12.6236190612058, 12.6244523880285, 12.6252857148512,
12.6261190416739, 12.6269523684966, 12.6277856953192, 12.6286190221419,
12.6294523489646, 12.6302856757873, 12.63111900261, 12.6319523294327,
12.6327856562554, 12.633618983078, 12.6344523099007, 12.6352856367234,
12.6361189635461, 12.6369522903688, 12.6377856171915, 12.6386189440141,
12.6394522708368, 12.6402855976595, 12.6411189244822, 12.6419522513049,
12.6427855781276, 12.6436189049503, 12.6444522317729, 12.6452855585956,
12.6461188854183, 12.646952212241, 12.6477855390637, 12.6486188658864,
12.649452192709, 12.6502855195317, 12.6511188463544, 12.6519521731771,
12.6527854999998, 12.6536188268225, 12.6544521536452, 12.6552854804678,
12.6561188072905, 12.6569521341132, 12.6577854609359, 12.6586187877586,
12.6594521145813, 12.6602854414039, 12.6611187682266, 12.6619520950493,
12.662785421872, 12.6636187486947, 12.6644520755174, 12.6652854023401,
12.6661187291627, 12.6669520559854, 12.6677853828081, 12.6686187096308,
12.6694520364535, 12.6702853632762, 12.6711186900988, 12.6719520169215,
12.6727853437442, 12.6736186705669, 12.6744519973896, 12.6752853242123,
12.6761186510349, 12.6769519778576, 12.6777853046803, 12.678618631503,
12.6794519583257, 12.6802852851484, 12.6811186119711, 12.6819519387937,
12.6827852656164, 12.6836185924391, 12.6844519192618, 12.6852852460845,
12.6861185729072, 12.6869518997298, 12.6877852265525, 12.6886185533752,
12.6894518801979, 12.6902852070206, 12.6911185338433, 12.691951860666,
12.6927851874886, 12.6936185143113, 12.694451841134, 12.6952851679567,
12.6961184947794, 12.6969518216021, 12.6977851484247, 12.6986184752474,
12.6994518020701, 12.7002851288928, 12.7011184557155, 12.7019517825382,
12.7027851093609, 12.7036184361835, 12.7044517630062, 12.7052850898289,
12.7061184166516, 12.7069517434743, 12.707785070297, 12.7086183971196,
12.7094517239423, 12.710285050765, 12.7111183775877, 12.7119517044104,
12.7127850312331, 12.7136183580558, 12.7144516848784, 12.7152850117011,
12.7161183385238, 12.7169516653465, 12.7177849921692, 12.7186183189919,
12.7194516458145, 12.7202849726372, 12.7211182994599, 12.7219516262826,
12.7227849531053, 12.723618279928, 12.7244516067506, 12.7252849335733,
12.726118260396, 12.7269515872187, 12.7277849140414, 12.7286182408641,
12.7294515676868, 12.7302848945094, 12.7311182213321, 12.7319515481548,
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12.7361181822682, 12.7369515090909, 12.7377848359136, 12.7386181627363,
12.739451489559, 12.7402848163817, 12.7411181432043, 12.741951470027,
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12.7461181041404, 12.7469514309631, 12.7477847577858, 12.7486180846085,
12.7494514114312, 12.7502847382539, 12.7511180650766, 12.7519513918992,
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12.7594513333034, 12.7602846601261, 12.7611179869488, 12.7619513137715,
12.7627846405941, 12.7636179674168, 12.7644512942395, 12.7652846210622,
12.7661179478849, 12.7669512747076, 12.7677846015302, 12.7686179283529,
12.7694512551756, 12.7702845819983, 12.771117908821, 12.7719512356437,
12.7727845624663, 12.773617889289, 12.7744512161117, 12.7752845429344,
12.7761178697571, 12.7769511965798, 12.7777845234025, 12.7786178502251,
12.7794511770478, 12.7802845038705, 12.7811178306932, 12.7819511575159,
12.7827844843386, 12.7836178111612, 12.7844511379839, 12.7852844648066,
12.7861177916293, 12.786951118452, 12.7877844452747, 12.7886177720974,
12.78945109892, 12.7902844257427, 12.7911177525654, 12.7919510793881,
12.7927844062108, 12.7936177330335, 12.7944510598561, 12.7952843866788,
12.7961177135015, 12.7969510403242, 12.7977843671469, 12.7986176939696,
12.7994510207923), value = c(17.3893229166667, 17.394140625,
17.3994791666667, 17.3966145833333, 17.397265625, 17.4009114583333,
17.4036458333333, 17.400390625, 17.3940104166667, 17.3908854166667,
17.3873697916667, 17.3858072916667, 17.3841145833333, 17.3834635416667,
17.383984375, 17.3837239583333, 17.3838541666667, 17.3850260416667,
17.3904947916667, 17.3954427083333, 17.39375, 17.3897135416667,
17.387109375, 17.3890625, 17.3876302083333, 17.385546875, 17.3850260416667,
17.390234375, 17.39921875, 17.4076822916667, 17.4131510416667,
17.41484375, 17.4111979166667, 17.402734375, 17.3953125, 17.3915364583333,
17.3934895833333, 17.3923177083333, 17.3938802083333, 17.3967447916667,
17.398828125, 17.4, 17.396484375, 17.4, 17.39921875, 17.4032552083333,
17.4138020833333, 17.4260416666667, 17.4364583333333, 17.4458333333333,
17.4639322916667, 17.491015625, 17.5239583333333, 17.5647135416667,
17.6229166666667, 17.6997395833333, 17.7994791666667, 17.916015625,
18.0544270833333, 18.2184895833333, 18.4170572916667, 18.6494791666667,
18.914453125, 19.2151041666667, 19.5665364583333, 19.9688802083333,
20.4143229166667, 20.8876302083333, 21.3850260416667, 21.9104166666667,
22.4467447916667, 23.0069010416667, 23.5716145833333, 24.1360677083333,
24.6528645833333, 25.1217447916667, 25.5454427083333, 25.9471354166667,
26.2817708333333, 26.5583333333333, 26.7454427083333, 26.8537760416667,
26.9045572916667, 26.889453125, 26.82734375, 26.6755208333333,
26.442578125, 26.1438802083333, 25.7912760416667, 25.437109375,
25.0861979166667, 24.7126302083333, 24.262890625, 23.73359375,
23.1990885416667, 22.7178385416667, 22.28359375, 21.8391927083333,
21.3856770833333, 20.9497395833333, 20.56640625, 20.2286458333333,
19.9221354166667, 19.6524739583333, 19.3998697916667, 19.1759114583333,
18.9670572916667, 18.7893229166667, 18.640625, 18.5109375, 18.401171875,
18.3026041666667, 18.2216145833333, 18.1454427083333, 18.0764322916667,
18.0162760416667, 17.9623697916667, 17.9102864583333, 17.8688802083333,
17.8309895833333, 17.8029947916667, 17.7690104166667, 17.7415364583333,
17.7149739583333, 17.693359375, 17.6713541666667, 17.6526041666667,
17.631640625, 17.6157552083333, 17.6013020833333, 17.5877604166667,
17.5740885416667, 17.5670572916667, 17.55703125, 17.545703125,
17.5307291666667, 17.527734375, 17.5272135416667, 17.5216145833333,
17.5140625, 17.5040364583333, 17.4944010416667, 17.4796875, 17.469921875,
17.4647135416667, 17.4657552083333, 17.46640625, 17.4638020833333,
17.4580729166667, 17.4485677083333, 17.4446614583333, 17.4430989583333,
17.4475260416667, 17.4428385416667, 17.4401041666667, 17.433984375,
17.4352864583333, 17.4342447916667, 17.4309895833333, 17.42890625,
17.4265625, 17.4248697916667, 17.42109375, 17.4109375, 17.4052083333333,
17.403125, 17.4092447916667, 17.413671875, 17.4153645833333,
17.4123697916667, 17.4123697916667, 17.4091145833333, 17.4052083333333,
17.401953125, 17.4052083333333, 17.40703125, 17.410546875, 17.4084635416667,
17.4096354166667, 17.4084635416667, 17.4135416666667, 17.4209635416667,
17.42265625, 17.42265625, 17.4223958333333, 17.4248697916667,
17.418359375, 17.4127604166667, 17.4125, 17.4184895833333, 17.4180989583333,
17.4111979166667, 17.4076822916667, 17.4158854166667, 17.425390625,
17.4279947916667, 17.424609375, 17.4229166666667, 17.4147135416667,
17.40625, 17.4014322916667, 17.4071614583333, 17.4125, 17.416796875,
17.415234375, 17.4084635416667, 17.402734375, 17.4018229166667,
17.4032552083333, 17.4009114583333, 17.40078125, 17.40078125,
17.4015625, 17.4002604166667, 17.4006510416667, 17.4001302083333,
17.398046875, 17.399609375, 17.4014322916667, 17.4, 17.39765625,
17.394140625, 17.3958333333333, 17.3985677083333, 17.399609375,
17.3979166666667, 17.3924479166667, 17.3860677083333, 17.3852864583333,
17.3834635416667, 17.3805989583333, 17.3751302083333, 17.3782552083333,
17.3834635416667, 17.3848958333333, 17.3802083333333, 17.3809895833333,
17.3842447916667, 17.3846354166667, 17.3779947916667, 17.3703125,
17.372265625, 17.3786458333333, 17.3860677083333, 17.38203125,
17.3813802083333, 17.38203125, 17.3881510416667, 17.38984375,
17.394921875, 17.3963541666667, 17.3998697916667, 17.3963541666667,
17.3932291666667, 17.3854166666667, 17.3725260416667, 17.3647135416667,
17.36328125, 17.372265625, 17.3756510416667, 17.380078125, 17.3766927083333,
17.378515625, 17.37578125, 17.382421875, 17.38359375, 17.379296875,
17.3759114583333, 17.37578125, 17.3803385416667, 17.378515625,
17.3837239583333, 17.3829427083333, 17.38359375, 17.3768229166667,
17.3790364583333, 17.380078125, 17.3846354166667, 17.3837239583333,
17.3869791666667, 17.3813802083333, 17.3889322916667, 17.388671875,
17.39375, 17.3911458333333, 17.3891927083333, 17.3889322916667,
17.386328125, 17.3830729166667, 17.3783854166667, 17.3748697916667,
17.3796875, 17.3830729166667, 17.383203125, 17.3755208333333,
17.37421875, 17.371875, 17.3735677083333, 17.37109375, 17.373046875,
17.3774739583333, 17.3782552083333, 17.3748697916667, 17.3764322916667,
17.3807291666667, 17.3876302083333, 17.3846354166667, 17.3802083333333,
17.376171875, 17.3727864583333, 17.3735677083333, 17.3796875,
17.3864583333333, 17.3876302083333, 17.3845052083333, 17.3850260416667,
17.3880208333333, 17.3891927083333, 17.3880208333333, 17.3830729166667,
17.3782552083333, 17.3765625, 17.379296875, 17.3829427083333,
17.3869791666667, 17.3881510416667, 17.384765625, 17.3763020833333,
17.376953125, 17.3786458333333, 17.3817708333333, 17.3821614583333,
17.3859375, 17.3876302083333, 17.3837239583333, 17.381640625,
17.37890625, 17.3802083333333, 17.3825520833333, 17.3881510416667,
17.3888020833333, 17.3864583333333, 17.3825520833333, 17.3834635416667,
17.386328125, 17.3854166666667, 17.384375, 17.3852864583333,
17.390234375, 17.3916666666667, 17.38828125, 17.3891927083333,
17.3901041666667, 17.3950520833333, 17.3963541666667, 17.3970052083333,
17.3907552083333, 17.3846354166667, 17.3760416666667, 17.3743489583333
)), row.names = 15002:15361, class = "data.frame")
(p.s the question here: R-package(baseline) application to sample dataset seems to have a similar problem, but doesn't address how to turn simple x,y data into the format required by the baseline package).

The baseline package expects spectra to appear in rows, but your code creates a matrix with the spectrum in a single column. If you change the conversion from data.frame to matrix to the following it should work:
baseline(matrix(y, nrow=1))
The problem was caused by two things, using as.matrix(), which does not take the arguments you need, and using byrow=T instead of nrow=1. byrow controls the direction in which the matrix is filled, either by rows or by columns, but has no effect on the output dimensions.
The extra fuzz in the milk data is not helping here, so I will remove it in the next package update. I will also look into the possibility of allowing single spectra to be handled in vector format instead of explicitly forcing matrix input.
P.S. I was able to copy out your data with a tiny extra effort, but suspect that you need the raw data to directly copy-paste from this page as the dput line contains som subsetting.

understanding the output of str function in R

I use the str to print out information for a calculate variable
str(samples)
'mcmc' num [1:1000, 1:228] 0.1079 -0.2367 -0.0757 -0.3414 -0.3382 ...
- attr(*, "dimnames")=List of 2
..$ : NULL
..$ : chr [1:228] "B[1,1,1]" "B[2,1,1]" "B[3,1,1]" "B[4,1,1]" ...
- attr(*, "mcpar")= num [1:3] 20005 25000 5
But how to read these information, or what does this output can tell us? For instance, the third component is attr(*, "mcpar")= num [1:3] 20005 25000 5, what does it mean?

The attr implies there is an attribute named 'mcpar' which is a numeric vector
attributes(samples)
returns a list of all the attributes of the samples i.e. it will return dimnames as one attribute and the 'mcpar' as another one
According to documentation
The ‘mcpar’ attribute of an MCMC object gives the start iteration the end iteration and the thinning interval of the chain.

unable to create a cluster/plan to a remote server in R

Trying (still) to get a cluster running. I have two Linux (Ubuntu) computers, the server is "laptop". Pretty sure ssh works, with key authentication, I can ssh to "laptop" without a password from command line. ssh_exec_wait works, e.g.,
session <- ssh_connect("laptop")
a <- ssh_exec_wait(session, command = "whoami")
ssh_disconnect(session)
works. I've gone through the doc (A future for R), works fine until I get to cluster futures.
plan(cluster, workers = c("localhost"))
works fine, but
plan(cluster, workers = c("laptop"))
gives the error:
Warning: remote port forwarding failed for listen port 11968
List of 2
$ node_idx: int 1
$ node :List of 5
..$ con : 'sockconn' int 3
.. ..- attr(*, "conn_id")=<externalptr>
..$ host : chr "laptop"
.. ..- attr(*, "localhost")= logi FALSE
..$ rank : int 1
..$ rshlogfile : NULL
..$ session_info:List of 6
.. ..$ r :List of 15
.. .. ..$ platform : chr "x86_64-pc-linux-gnu"
.. .. ..$ arch : chr "x86_64"
.. .. ..$ os : chr "linux-gnu"
.. .. ..$ system : chr "x86_64, linux-gnu"
.. .. ..$ status : chr ""
.. .. ..$ major : chr "3"
.. .. ..$ minor : chr "6.3"
.. .. ..$ year : chr "2020"
.. .. ..$ month : chr "02"
.. .. ..$ day : chr "29"
.. .. ..$ svn rev : chr "77875"
.. .. ..$ language : chr "R"
.. .. ..$ version.string: chr "R version 3.6.3 (2020-02-29)"
.. .. ..$ nickname : chr "Holding the Windsock"
.. .. ..$ os.type : chr "unix"
.. ..$ system :List of 8
.. .. ..$ sysname : chr "Linux"
.. .. ..$ release : chr "5.3.0-46-generic"
.. .. ..$ version : chr "#38~18.04.1-Ubuntu SMP Tue Mar 31 04:17:56 UTC 2020"
.. .. ..$ nodename : chr "laptop"
.. .. ..$ machine : chr "x86_64"
.. .. ..$ login : chr "mark"
.. .. ..$ user : chr "mark"
.. .. ..$ effective_user: chr "mark"
.. ..$ libs : chr [1:4] "/home/mark/R/x86_64-pc-linux-gnu-library/3.6" "/usr/local/lib/R/site-library" "/usr/lib/R/site-library" "/usr/lib/R/library"
.. ..$ pkgs : NULL
.. ..$ pwd : chr "/home/mark"
.. ..$ process:List of 1
.. .. ..$ pid: int 2809
..- attr(*, "class")= chr "SOCKnode"
Error: Initialization of plan() failed, because the test future used for validation failed. The reason was: Unexpected result (of class ‘NULL’ != ‘FutureResult’) retrieved for ClusterFuture future (label = ‘future-plan-test’, expression = ‘NA’): . This suggests that the communication with ClusterFuture worker (‘SOCKnode’ #1) is out of sync.
I assume the first line is the real error message:
Warning: remote port forwarding failed for listen port 11968
Do I need to manually set the port?

In my experience, the warning
Warning: remote port forwarding failed for listen port 11968
is caused by a hanging R process on that port (it could be another process of course but it's likely that the future package created it). If you kill the process on laptop, the port should become available again.
You can check by manually running
ssh -R 11968:localhost:11968 laptop

How to reference .. .. elements in list in R?

How do you access list elements prefaced with double dots .. ..?
I am trying to isolate the $attr part of the html to help in another question into a variable, and then place it another mime variable. x$parts$attr gives me NULL.
Thanks for your help.
EXAMPLE
library(gmailr)
test_email <- mime()
x <- html_body(mime = test_email, body = "I wish I had a nice body")
str(x)
List of 5
$ parts :List of 2
..$ : NULL
..$ :List of 4
.. ..$ parts : list()
.. ..$ header:List of 2
.. .. ..$ MIME-Version: chr "1.0"
.. .. ..$ Date : chr "Sun, 24 May 2015 09:44:59 GMT"
.. ..$ body : chr "I wish I had a nice body"
.. ..$ attr :List of 3 # << HOW do I get this?
.. .. ..$ content_type: chr "text/html"
.. .. ..$ charset : chr "utf-8"
.. .. ..$ encoding : chr "base64"
.. ..- attr(*, "class")= chr "mime"

Try this:
str(x$parts[[2]]$attr)
List of 3
$ content_type: chr "text/html"
$ charset : chr "utf-8"
$ encoding : chr "base64"

R understanding and access a nested object by reading from str

Hi I have a nested object which I think contains tables. I used str to see how it looks like,
> str(test)
Formal class 'CuffData' [package "cummeRbund"] with 5 slots
..# DB :Formal class 'SQLiteConnection' [package "RSQLite"] with 5 slots
.. .. ..# Id :<externalptr>
.. .. ..# dbname : chr "C:/temp/cuffData.db"
.. .. ..# loadable.extensions: logi TRUE
.. .. ..# flags : int 6
.. .. ..# vfs : chr ""
..# tables :List of 6
.. ..$ mainTable : chr "genes"
.. ..$ dataTable : chr "geneData"
.. ..$ expDiffTable : chr "geneExpDiffData"
.. ..$ featureTable : chr "geneFeatures"
.. ..$ countTable : chr "geneCount"
.. ..$ replicateTable: chr "geneReplicateData"
..# filters: list()
..# type : chr "genes"
..# idField: chr "gene_id"
however when I tried to to read the table mainTable all I get is this,
> test#tables$mainTable
[1] "genes"
is there any way I can read what is in this table?
Not sure if I'm even interpreting the str output correctly though. I'm a newbie at this and I'm also wondering if there is a good tutorial on how to interpret objects like these in R? Examples would be even better.
thanks you much in advance.
Ahdee

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