R Slotnames
2021年11月14日Register here: http://gg.gg/wv9cl
*Setnames In R
*R Slotnames [This article was first published on YGC » R, and kindly contributed to R-bloggers]. (You can report issue about the content on this page here) Want to share your content on R-bloggers? click here if you have a blog, or here if you don’t.
hyperGTest compute Hypergeomtric p-values for over or under-representation of each GO term in the specified category among the specified gene set.
*geneSample* was used as an example.
After using hyperGTest to test GO terms for over-representation, I get the result which were shown below:
I want to know which subset of the input genes, which does not reported, represented in the significant GO term.
Introduction Statistical disclosure control (SDC) is an emerging field of research. More and more data on persons and establishments are collected by statistical organizations and almost all of these data holds confidential information. The demand for micro-data for. Objects from the Class. A virtual Class: No objects may be created from it. Class ’GARCHfit, directly.Class ’rGARCH, by class ’GARCHfit, distance 2. Object of class ’vector’ Holds data on the fitted model.
This can be done by using the genome wide annotation data, for human at this example, org.Hs.eg.db, for mapping Entrez gene IDs to GO IDs.
Useful S4 Methods in R. Here are a few functions that are useful when dealing with S4 objects: 1. The isS4 function: the isS4 function returns TRUE if the input argument is an S4 object. Code: isS4(emp2) Output: 2. The slotNames function: the slotNames function returns the names of all the slots in the input object. Code: slotNames(emp2. Loading the Matrix namespace “overloads” as.matrix and as.array in the base namespace by the equivalent of function(x) as(x, ’matrix’).Consequently, as.matrix(m) or as.array(m) will properly work when m inherits from the ’Matrix’ class - also for functions in package base and other packages. E.g., apply or outer can therefore be applied to ’Matrix’ matrices.
Since GO ontology is a directed acyclic graph, all genes that are annotated with a child GO term are also annotated with their parent terms. So, org.Hs.egGO2ALLEGS is using for mapping rather than org.Hs.egGO.
I am working with a R package called ’Seurat’ for single cell RNA-Seq analysis and I am trying to remove few genes in seuratobject (s4 class) from slot name ’data’. There are several slots in this object as well that stores information associated to the slot ’data’.
In the example above, we can get the corresponding gene set by:
The gene set can further map to other identifiers or annotation data by biomaRt package.Related Posts
*October 12, 2010 — ClusterProfiles (0)
*May 28, 2010 — GOSemSim: an R package for measuring semantic similarity among GO terms and gene products (1)
*August 11, 2008 — GOSemSim (0)
*October 15, 2010 — The S3 OOP system (0)
*October 11, 2010 — highlight R syntax in wordpress using wp-codebox (0)
*October 20, 2007 — 使用R/BioC画网络图 (0)
*September 14, 2007 — 在Ubuntu中安装R/BioConductor (0)
*October 8, 2010 — dotplot (0)
*September 25, 2010 — unorder factor in R (0)
*September 18, 2010 — R中概率分布的几个函数 (0)To leave a comment for the author, please follow the link and comment on their blog: YGC » R.R-bloggers.com offers daily e-mail updates about R news and tutorials about learning R and many other topics. Click here if you’re looking to post or find an R/data-science job. Want to share your content on R-bloggers? click here if you have a blog, or here if you don’t. The Names of an Object
Functions to get or set the names of an object.KeywordsattributeUsageArgumentsx
an R object.value
a character vector of up to the same length as x, or NULL.Details
names is a generic accessor function, and names<- is a generic replacement function. The default methods get and set the ’names’ attribute of a vector (including a list) or pairlist.
For an environmentenv, names(env) gives the names of the corresponding list, i.e., names(as.list(env, all.names = TRUE)) which are also given by ls(env, all.names = TRUE, sorted = FALSE). If the environment is used as a hash table, names(env) are its “keys”.
If value is shorter than x, it is extended by character NAs to the length of x.
It is possible to update just part of the names attribute via the general rules: see the examples. This works because the expression there is evaluated as z <- ’names<-’(z, ’[<-’(names(z), 3, ’c2’)).
The name ’ is special: it is used to indicate that there is no name associated with an element of a (atomic or generic) vector. Subscripting by ’ will match nothing (not even elements which have no name).
A name can be character NA, but such a name will never be matched and is likely to lead to confusion.
Both are primitive functions.Value
For names, NULL or a character vector of the same length as x. (NULL is given if the object has no names, including for objects of types which cannot have names.) For an environment, the length is the number of objects in the environment but the order of the names is arbitrary.
For names<-, the updated object. (Note that the value of names(x) <- value is that of the assignment, value, not the return value from the left-hand side.)Note
For vectors, the names are one of the attributes with restrictions on the possible values. For pairlists, the names are the tags and converted to and from a character vector.
For a one-dimensional array the names attribute really is dimnames[[1]].
Formally classed aka “S4” objects typically have slotNames() (and no names()).References
Becker, R. A., Chambers, J. M. and Wilks, A. R. (1988) The New S Language. Wadsworth & Brooks/Cole.See Also
slotNames, dimnames.Aliases
*names
*names.default
*names<-
*names<-.defaultExampleslibrary(base)# NOT RUN {# print the names attribute of the islands data setnames(islands)# remove the names attributenames(islands) <- NULLislandsrm(islands) # remove the copy madez <- list(a = 1, b = ’c’, c = 1:3)names(z)# change just the name of the third element.names(z)[3] <- ’c2’zz <- 1:3names(z)## assign just one namenames(z)[2] <- ’b’z# }Setnames In R Documentation reproduced from package base, version 3.6.2, License: Part of R 3.6.2 Community examplesrichie@datacamp.com at Jan 17, 2017 base v3.3.2
A better way to remove the `names` attribute is to use [`unname()`](https://www.rdocumentation.org/packages/base/topics/unname).```{r}unname(islands)```The main advantage of having names is that it gives you an easy-to-read way of subsetting.```{r}islands[c(’South America’, ’Southampton’)]```Or, more fancily, you can use a regular expression to extract all islands with names begining with `’A’`, for example.```{r}islands[grepl(’^A’, names(islands))]```Lists can also have names.```{r}(l <- list(a = 1, b = letters[1:5], c = list(d = 1:3)))names(l) # only the top level element names, not ’d’names(unlist(l)) # unlist gives a name for every element```You can overwrite all the names.```{r}(l <- list(a = 1, b = letters[1:5], c = list(d = 1:3)))names(l) <- LETTERS[1:3]l```… or just some of them.```{r}(l <- list(a = 1, b = letters[1:5], c = list(d = 1:3)))names(l)[1:2] <- c(’Alpha’, ’Beta’)l```Setting names on an object, then returning that object can be done in a single step using [`setNames()`](https://www.rdocumentation.org/packages/stats/topics/setNames).```{r}(l <- list(a = 1, b = letters[1:5], c = list(d = 1:3)))setNames(l, c(’Alef’, ’Bet’, ’Gimel’))```If an object has no names, then the `names()` function returns `NULL`.```{r}v <- 1:3names(v)```If an object has some names, then the names function returns a character vector with missing values where there are no names.```{r}v <- 1:3names(v)[2] <- ’2nd’names(v)v``` R Slotnames API documentation
Register here: http://gg.gg/wv9cl
https://diarynote.indered.space
*Setnames In R
*R Slotnames [This article was first published on YGC » R, and kindly contributed to R-bloggers]. (You can report issue about the content on this page here) Want to share your content on R-bloggers? click here if you have a blog, or here if you don’t.
hyperGTest compute Hypergeomtric p-values for over or under-representation of each GO term in the specified category among the specified gene set.
*geneSample* was used as an example.
After using hyperGTest to test GO terms for over-representation, I get the result which were shown below:
I want to know which subset of the input genes, which does not reported, represented in the significant GO term.
Introduction Statistical disclosure control (SDC) is an emerging field of research. More and more data on persons and establishments are collected by statistical organizations and almost all of these data holds confidential information. The demand for micro-data for. Objects from the Class. A virtual Class: No objects may be created from it. Class ’GARCHfit, directly.Class ’rGARCH, by class ’GARCHfit, distance 2. Object of class ’vector’ Holds data on the fitted model.
This can be done by using the genome wide annotation data, for human at this example, org.Hs.eg.db, for mapping Entrez gene IDs to GO IDs.
Useful S4 Methods in R. Here are a few functions that are useful when dealing with S4 objects: 1. The isS4 function: the isS4 function returns TRUE if the input argument is an S4 object. Code: isS4(emp2) Output: 2. The slotNames function: the slotNames function returns the names of all the slots in the input object. Code: slotNames(emp2. Loading the Matrix namespace “overloads” as.matrix and as.array in the base namespace by the equivalent of function(x) as(x, ’matrix’).Consequently, as.matrix(m) or as.array(m) will properly work when m inherits from the ’Matrix’ class - also for functions in package base and other packages. E.g., apply or outer can therefore be applied to ’Matrix’ matrices.
Since GO ontology is a directed acyclic graph, all genes that are annotated with a child GO term are also annotated with their parent terms. So, org.Hs.egGO2ALLEGS is using for mapping rather than org.Hs.egGO.
I am working with a R package called ’Seurat’ for single cell RNA-Seq analysis and I am trying to remove few genes in seuratobject (s4 class) from slot name ’data’. There are several slots in this object as well that stores information associated to the slot ’data’.
In the example above, we can get the corresponding gene set by:
The gene set can further map to other identifiers or annotation data by biomaRt package.Related Posts
*October 12, 2010 — ClusterProfiles (0)
*May 28, 2010 — GOSemSim: an R package for measuring semantic similarity among GO terms and gene products (1)
*August 11, 2008 — GOSemSim (0)
*October 15, 2010 — The S3 OOP system (0)
*October 11, 2010 — highlight R syntax in wordpress using wp-codebox (0)
*October 20, 2007 — 使用R/BioC画网络图 (0)
*September 14, 2007 — 在Ubuntu中安装R/BioConductor (0)
*October 8, 2010 — dotplot (0)
*September 25, 2010 — unorder factor in R (0)
*September 18, 2010 — R中概率分布的几个函数 (0)To leave a comment for the author, please follow the link and comment on their blog: YGC » R.R-bloggers.com offers daily e-mail updates about R news and tutorials about learning R and many other topics. Click here if you’re looking to post or find an R/data-science job. Want to share your content on R-bloggers? click here if you have a blog, or here if you don’t. The Names of an Object
Functions to get or set the names of an object.KeywordsattributeUsageArgumentsx
an R object.value
a character vector of up to the same length as x, or NULL.Details
names is a generic accessor function, and names<- is a generic replacement function. The default methods get and set the ’names’ attribute of a vector (including a list) or pairlist.
For an environmentenv, names(env) gives the names of the corresponding list, i.e., names(as.list(env, all.names = TRUE)) which are also given by ls(env, all.names = TRUE, sorted = FALSE). If the environment is used as a hash table, names(env) are its “keys”.
If value is shorter than x, it is extended by character NAs to the length of x.
It is possible to update just part of the names attribute via the general rules: see the examples. This works because the expression there is evaluated as z <- ’names<-’(z, ’[<-’(names(z), 3, ’c2’)).
The name ’ is special: it is used to indicate that there is no name associated with an element of a (atomic or generic) vector. Subscripting by ’ will match nothing (not even elements which have no name).
A name can be character NA, but such a name will never be matched and is likely to lead to confusion.
Both are primitive functions.Value
For names, NULL or a character vector of the same length as x. (NULL is given if the object has no names, including for objects of types which cannot have names.) For an environment, the length is the number of objects in the environment but the order of the names is arbitrary.
For names<-, the updated object. (Note that the value of names(x) <- value is that of the assignment, value, not the return value from the left-hand side.)Note
For vectors, the names are one of the attributes with restrictions on the possible values. For pairlists, the names are the tags and converted to and from a character vector.
For a one-dimensional array the names attribute really is dimnames[[1]].
Formally classed aka “S4” objects typically have slotNames() (and no names()).References
Becker, R. A., Chambers, J. M. and Wilks, A. R. (1988) The New S Language. Wadsworth & Brooks/Cole.See Also
slotNames, dimnames.Aliases
*names
*names.default
*names<-
*names<-.defaultExampleslibrary(base)# NOT RUN {# print the names attribute of the islands data setnames(islands)# remove the names attributenames(islands) <- NULLislandsrm(islands) # remove the copy madez <- list(a = 1, b = ’c’, c = 1:3)names(z)# change just the name of the third element.names(z)[3] <- ’c2’zz <- 1:3names(z)## assign just one namenames(z)[2] <- ’b’z# }Setnames In R Documentation reproduced from package base, version 3.6.2, License: Part of R 3.6.2 Community examplesrichie@datacamp.com at Jan 17, 2017 base v3.3.2
A better way to remove the `names` attribute is to use [`unname()`](https://www.rdocumentation.org/packages/base/topics/unname).```{r}unname(islands)```The main advantage of having names is that it gives you an easy-to-read way of subsetting.```{r}islands[c(’South America’, ’Southampton’)]```Or, more fancily, you can use a regular expression to extract all islands with names begining with `’A’`, for example.```{r}islands[grepl(’^A’, names(islands))]```Lists can also have names.```{r}(l <- list(a = 1, b = letters[1:5], c = list(d = 1:3)))names(l) # only the top level element names, not ’d’names(unlist(l)) # unlist gives a name for every element```You can overwrite all the names.```{r}(l <- list(a = 1, b = letters[1:5], c = list(d = 1:3)))names(l) <- LETTERS[1:3]l```… or just some of them.```{r}(l <- list(a = 1, b = letters[1:5], c = list(d = 1:3)))names(l)[1:2] <- c(’Alpha’, ’Beta’)l```Setting names on an object, then returning that object can be done in a single step using [`setNames()`](https://www.rdocumentation.org/packages/stats/topics/setNames).```{r}(l <- list(a = 1, b = letters[1:5], c = list(d = 1:3)))setNames(l, c(’Alef’, ’Bet’, ’Gimel’))```If an object has no names, then the `names()` function returns `NULL`.```{r}v <- 1:3names(v)```If an object has some names, then the names function returns a character vector with missing values where there are no names.```{r}v <- 1:3names(v)[2] <- ’2nd’names(v)v``` R Slotnames API documentation
Register here: http://gg.gg/wv9cl
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