Removing/parsing rows from a matrix in R - r

I'm trying to parse out specific rows from a data matrix. The actual data is numeric and comprises a single column. I've used this method before for other data, and I cannot figure out why this isn't working.
csize = data.matrix(wc$Csize)
length(csize)
[1] 134
csize[-111,][-110,][-107,][-105,][-104,][-94,][-88,][-68,][-58,][-57,][-56,][-30,][-22,][,1]
Error in csize[-111, ][-110, ] : incorrect number of dimensions
Here is the code that does work for me with other data:
w.pc.res <- prcomp(sizeshapew)
w.pcdata <- w.pc.res$x
length(w.pcdata)
[1] 11792
w.pcdata[-111,][-110,][-107,][-105,][-104,][-94,][-88,][-68,][-58,][-57,][-56,][-30,][-22,][,1]


I don't think it likes the multiple subscripting, just provide the subscripts in a vector e.g csize[c(-111, -110, ...),]

Related

How to extract components from an object of class "spec"?

I am trying to construct a table of power spectra and run into this problem:
Define the table:
V <- tibble(month=double(),day=double(),hour=double(),minutes=double(),
frequency=double(),power=double(),period=double())
compute the spectrum:
S <- spec.pgram(Spec2d$Inst,spans=windowSize,log="yes")
which creates an object of class "spec"
I need to extract the data from S and put it into V. When I try:
V$frequency <- S$freq
I get this error message:
Error: Assigned data `S$freq` must be compatible with existing data.
x Existing data has 0 rows.
x Assigned data has 48 rows.
ℹ Only vectors of size 1 are recycled.
which doesn't make sense to me. I have tried to coerce S$freq into different different types of objects but nothing works.
S$freq is a vector of length 48 as in the error message
What is going on? Is there a workaround?

Don't initialise the dataframe/tibble first. Try :
S <- spec.pgram(Spec2d$Inst,spans=windowSize,log="yes")
V <- data.frame(frequency = S$freq)

how to find common columns between 2 data set in r?

I have two data sets: "datExprSTLMS" which its dimension is 53*17237 and "datExprSTF" which its dimension is 99*22144. In two data sets, some columns(gene_names) are common. Based on using match() between colnames of two data sets I have founded 15711(TRUE) gene_name as intersecting genes between them. Now, I would like to provide a subset of "datExprSTLMS" so that the dimension of "datExprSTLMS" will be 53*15711. For this purpose I wrote below code:
dim(datExprSTF)
#[1] 99 22144
dim(datExprSTLMS)
#[1] 53 17237
TCGA2STF <- match(colnames(datExprSTLMS), colnames(datExprSTF))
table(is.finite(TCGA2STF))
#FALSE TRUE
#1526 15711
#delete NA(mismatch gene_names which in my case are 1526)
TCGA2STF_final <- Filter(function(x)!all(is.na(x)), TCGA2STF)
datExprSTLMS_final <- as.data.frame(datExprSTLMS[,TCGA2STF_final])
but after running the last line of my code I get below Error:
Error in datExprSTLMS[, TCGA2STF_final] : subscript out of bounds
I write my code in the R language. I need to guide

We can use intersect to find common columns between two data sets and then use them to subset datExprSTLMS
datExprSTLMS[, intersect(colnames(datExprSTLMS), colnames(datExprSTF))]

R in counting data

Right now I'm trying to do a bell curve on a file called output9.csv on my.
Here is my code, I want to uses z score to detect outliers, and uses the difference between the value and mean of the data set.The difference is compared with standard deviation to find the outliers. va
#DATA LOAD
data <- read.csv('output9.csv')
height <- data$Height
hist(height) #histogram
#POPULATION PARAMETER CALCULATIONS
pop_sd <- sd(height)*sqrt((length(height)-1)/(length(height)))
pop_mean <- mean(height)
But I have this error after I tried the histogram part,
> hist(height)
Error in hist.default(height) : 'x' must be numeric
how should I fix this?

Since I don't have your data I can only guess. Can you provide it? Or at least a portion of it?
What class is your data? You can use class(data) to find out. The most common way is to have table-like data in data.frames. To subset one of your columns to use it for the hist you can use the $ operator. Be sure you subset on a column that actually exists. You can use names(data) (if data is a data.frame) to find out what columns exist in your data. Use nrow(data) to find out how many rows there are in your data.
After extracting your height you can go further. First check that your height object is numeric and has something in it. You can use class(height) to find out.
As you posted in your comment you have the following names
names(data)
# [1] "Host" "TimeStamp" "TimeZone" "Command" "RequestLink" "HTTP" [7] "ReplyCode" "Bytes"
Therefore you can extract your height with
height <- data$Bytes
Did you try to convert it to numeric? as.numeric(height) might do the trick. as.numeric() can coerce all things that are stored as characters but might also be numbers automatically. Try as.numeric("3") as an example.
Here an example I made up.
height <- c(1,1,2,3,1)
class(height)
# [1] "numeric"
hist(height)
This works just fine, because the data is numeric.
In the following the data are numbers but formatted as characters.
height_char <- c("1","1","2","3","1")
class(height_char)
# [1] "character"
hist(height_char)
# Error in hist.default(height) : 'x' must be numeric
So you have to coerce it first:
hist(as.numeric(height_char))
..and then it works fine.
For future questions: Try to give Minimal, Complete, and Verifiable Examples.

xgb.DMatrix Error: The length of labels must equal to the number of rows in the input data

I am using xgboost in R.
I created the xgb matrix fine using a matrix as input, but when I reduce the number in columns in the matrix data, I receive an error.
This works:
> dim(ctt1)
[1] 6401 5901
> xgbmat1 <- xgb.DMatrix(
Matrix(data.matrix(ctt1)),
label = as.matrix(as.numeric(data$V2)) - 1
)
This does not:
> dim(ctt1[,nr])
[1] 6401 1048
xgbmat1 <- xgb.DMatrix(
Matrix(data.matrix(ctt1[,nr])),
label = as.matrix(as.numeric(data$V2)) - 1)
Error in xgb.setinfo(dmat, names(p), p[[1]]) :
The length of labels must equal to the number of rows in the input data

In my case I fixed this error by changing assign operation:
labels <- df_train$target_feature

It turns out that by removing some columns, there are some rows with all 0s, and could not contribute to model.

For sparse matrices, xgboost R interface uses the CSC format creation method. The problem currently is that this method automatically determines the number of rows from the existing non-sparse values, and any completely sparse rows at the end are not counted in. A similar loss of completely sparse columns at the end can happen with the CSR sparse format. For more details see xgboost issue #1223 and also wikipedia on the sparse matrix formats.

The proper way for creating the DBMatrix Like
xgtrain <- xgb.DMatrix(data = as.matrix(X_train[,-5]), label = `X_train$item_cnt_month)`
drop the label column in data parameter and use same data set for create label column in index five i have item_cnt_month i drop it at run time and use same data set for referring label column

Before splitting your data, you need to turn it into a data frame.
For Exemplo:
data <- read.csv(...)
data = as.data.frame(data)
Now you can set your train data and test data to use in your "sparse.model.matrix" and "xgb.DMatrix".

R understanding behaviour of as.matrix and matrix while plotting an image

I am reading data from MNIST handwritten digit dataset. Its first column is the digit label and rest 784 columns (28 X 28) are pixel values. Pixel values are between [0, 255]. Thus, there are a total of 1+784=785 columns. To plot a row as an image, I have to convert the 784 pixel values into a matrix of 28X28. In this conversion process, I am not clear about the behaviour of as.matrix() and matrix() functions. The code and comments are as follows:
> train <- read.csv("train.csv", header=TRUE)
# Read 2nd row. Ignore the label col and read rest of 784 columns
> data<-train[2,2:785]
# Convert data into matrix of 28X28
> data<-as.matrix(data,nrow=28,ncol=28)
> dim(data)
[1] 1 784 <= Failed to convert to 28X28
> class(data)
[1] "matrix" <= But class is matrix
# as.matrix() failed. Use matrix()
> data<-matrix(data,nrow=28,ncol=28)
> dim(data)
[1] 28 28 <= Matrix conversion success
Probably, the solution is to ignore as.matrix() altogether and just use matrix(). But, it so happens that in plotting the image as.matrix() does serve as a necessary intermediary. For example, the following code works to plot the image of digit zero:
train <- read.csv("train.csv", header=TRUE)
data<-train[2,2:785]
data<-as.matrix(data,nrow=28,ncol=28)
data<-matrix(data,nrow=28,ncol=28)
##Color ramp def.
colors<-c('white','black')
cus_col<-colorRampPalette(colors=colors)
image(1:28,1:28,data,main="IInd row",col=cus_col(256))
But, in the following code where I have removed as.matrix(), the code gives an error:
> train <- read.csv("train.csv", header=TRUE)
> data<-train[2,2:785]
> data<-matrix(data,nrow=28,ncol=28)
> ##Color ramp def.
> colors<-c('white','black')
> cus_col<-colorRampPalette(colors=colors)
> image(1:28,1:28,data,main="IInd row",col=cus_col(256))
Error in is.finite(z) : default method not implemented for type 'list'
I am unable to understand the role of as.matrix() and the meaning of this error. Kindly do let me know what is wrong.
EDITED
Here is what the first three rows of data look like:
label,pixel0,pixel1,pixel2,pixel3,pixel4,pixel5,pixel6,pixel7,pixel8,pixel9,pixel10,pixel11,pixel12,pixel13,pixel14,pixel15,pixel16,pixel17,pixel18,pixel19,pixel20,pixel21,pixel22,pixel23,pixel24,pixel25,pixel26,pixel27,pixel28,pixel29,pixel30,pixel31,pixel32,pixel33,pixel34,pixel35,pixel36,pixel37,pixel38,pixel39,pixel40,pixel41,pixel42,pixel43,pixel44,pixel45,pixel46,pixel47,pixel48,pixel49,pixel50,pixel51,pixel52,pixel53,pixel54,pixel55,pixel56,pixel57,pixel58,pixel59,pixel60,pixel61,pixel62,pixel63,pixel64,pixel65,pixel66,pixel67,pixel68,pixel69,pixel70,pixel71,pixel72,pixel73,pixel74,pixel75,pixel76,pixel77,pixel78,pixel79,pixel80,pixel81,pixel82,pixel83,pixel84,pixel85,pixel86,pixel87,pixel88,pixel89,pixel90,pixel91,pixel92,pixel93,pixel94,pixel95,pixel96,pixel97,pixel98,pixel99,pixel100,pixel101,pixel102,pixel103,pixel104,pixel105,pixel106,pixel107,pixel108,pixel109,pixel110,pixel111,pixel112,pixel113,pixel114,pixel115,pixel116,pixel117,pixel118,pixel119,pixel120,pixel121,pixel122,pixel123,pixel124,pixel125,pixel126,pixel127,pixel128,pixel129,pixel130,pixel131,pixel132,pixel133,pixel134,pixel135,pixel136,pixel137,pixel138,pixel139,pixel140,pixel141,pixel142,pixel143,pixel144,pixel145,pixel146,pixel147,pixel148,pixel149,pixel150,pixel151,pixel152,pixel153,pixel154,pixel155,pixel156,pixel157,pixel158,pixel159,pixel160,pixel161,pixel162,pixel163,pixel164,pixel165,pixel166,pixel167,pixel168,pixel169,pixel170,pixel171,pixel172,pixel173,pixel174,pixel175,pixel176,pixel177,pixel178,pixel179,pixel180,pixel181,pixel182,pixel183,pixel184,pixel185,pixel186,pixel187,pixel188,pixel189,pixel190,pixel191,pixel192,pixel193,pixel194,pixel195,pixel196,pixel197,pixel198,pixel199,pixel200,pixel201,pixel202,pixel203,pixel204,pixel205,pixel206,pixel207,pixel208,pixel209,pixel210,pixel211,pixel212,pixel213,pixel214,pixel215,pixel216,pixel217,pixel218,pixel219,pixel220,pixel221,pixel222,pixel223,pixel224,pixel225,pixel226,pixel227,pixel228,pixel229,pixel230,pixel231,pixel232,pixel233,pixel234,pixel235,pixel236,pixel237,pixel238,pixel239,pixel240,pixel241,pixel242,pixel243,pixel244,pixel245,pixel246,pixel247,pixel248,pixel249,pixel250,pixel251,pixel252,pixel253,pixel254,pixel255,pixel256,pixel257,pixel258,pixel259,pixel260,pixel261,pixel262,pixel263,pixel264,pixel265,pixel266,pixel267,pixel268,pixel269,pixel270,pixel271,pixel272,pixel273,pixel274,pixel275,pixel276,pixel277,pixel278,pixel279,pixel280,pixel281,pixel282,pixel283,pixel284,pixel285,pixel286,pixel287,pixel288,pixel289,pixel290,pixel291,pixel292,pixel293,pixel294,pixel295,pixel296,pixel297,pixel298,pixel299,pixel300,pixel301,pixel302,pixel303,pixel304,pixel305,pixel306,pixel307,pixel308,pixel309,pixel310,pixel311,pixel312,pixel313,pixel314,pixel315,pixel316,pixel317,pixel318,pixel319,pixel320,pixel321,pixel322,pixel323,pixel324,pixel325,pixel326,pixel327,pixel328,pixel329,pixel330,pixel331,pixel332,pixel333,pixel334,pixel335,pixel336,pixel337,pixel338,pixel339,pixel340,pixel341,pixel342,pixel343,pixel344,pixel345,pixel346,pixel347,pixel348,pixel349,pixel350,pixel351,pixel352,pixel353,pixel354,pixel355,pixel356,pixel357,pixel358,pixel359,pixel360,pixel361,pixel362,pixel363,pixel364,pixel365,pixel366,pixel367,pixel368,pixel369,pixel370,pixel371,pixel372,pixel373,pixel374,pixel375,pixel376,pixel377,pixel378,pixel379,pixel380,pixel381,pixel382,pixel383,pixel384,pixel385,pixel386,pixel387,pixel388,pixel389,pixel390,pixel391,pixel392,pixel393,pixel394,pixel395,pixel396,pixel397,pixel398,pixel399,pixel400,pixel401,pixel402,pixel403,pixel404,pixel405,pixel406,pixel407,pixel408,pixel409,pixel410,pixel411,pixel412,pixel413,pixel414,pixel415,pixel416,pixel417,pixel418,pixel419,pixel420,pixel421,pixel422,pixel423,pixel424,pixel425,pixel426,pixel427,pixel428,pixel429,pixel430,pixel431,pixel432,pixel433,pixel434,pixel435,pixel436,pixel437,pixel438,pixel439,pixel440,pixel441,pixel442,pixel443,pixel444,pixel445,pixel446,pixel447,pixel448,pixel449,pixel450,pixel451,pixel452,pixel453,pixel454,pixel455,pixel456,pixel457,pixel458,pixel459,pixel460,pixel461,pixel462,pixel463,pixel464,pixel465,pixel466,pixel467,pixel468,pixel469,pixel470,pixel471,pixel472,pixel473,pixel474,pixel475,pixel476,pixel477,pixel478,pixel479,pixel480,pixel481,pixel482,pixel483,pixel484,pixel485,pixel486,pixel487,pixel488,pixel489,pixel490,pixel491,pixel492,pixel493,pixel494,pixel495,pixel496,pixel497,pixel498,pixel499,pixel500,pixel501,pixel502,pixel503,pixel504,pixel505,pixel506,pixel507,pixel508,pixel509,pixel510,pixel511,pixel512,pixel513,pixel514,pixel515,pixel516,pixel517,pixel518,pixel519,pixel520,pixel521,pixel522,pixel523,pixel524,pixel525,pixel526,pixel527,pixel528,pixel529,pixel530,pixel531,pixel532,pixel533,pixel534,pixel535,pixel536,pixel537,pixel538,pixel539,pixel540,pixel541,pixel542,pixel543,pixel544,pixel545,pixel546,pixel547,pixel548,pixel549,pixel550,pixel551,pixel552,pixel553,pixel554,pixel555,pixel556,pixel557,pixel558,pixel559,pixel560,pixel561,pixel562,pixel563,pixel564,pixel565,pixel566,p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Difference is explained in the documentation.
https://stat.ethz.ch/R-manual/R-devel/library/base/html/matrix.html
Also all rows & columns of a matrix must have the same class (numeric, character, etc). In a dataframe, you can have some of each. Sometimes R is not able to convert different classes when using as.matrix()

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