annotate (version 1.50.0)

chrCats: Returns a list of chromosome locations from a MAP environment

Description

The chrCats function takes a data package that contains a MAP environment and returns a list that contains the locations for each gene (from the chromosome number to more specific locations if they're available). For example, the hgu95av2MAP environment gives the location, 14q22-q23, for Affymetrix identifier: 1114\_at. This function will return a list with one named element for 1114\_at and the values it will contain are 14, 14q, 14q2, 14q22, and 14q23 since the Affy id is located at each of those chromosome locations.

Usage

chrCats(data)
createMAPIncMat(data)
createLLChrCats(data)

Arguments

data

the data package (a character string)

Value

A named list with an element for each Affy id. The name will be the Affy id and the values will be the locations for that Affy id. If the Affy id had a location of NA in the MAP environment, then a list element is not returned for that Affy id.

Details

This function does a lot of string manipulation and there are a few known errors so I want to discuss them here in case someone else would like to improve on this function.

The first thing, chrCats, does is only allow one location for each Affymetrix identifier. If the MAP environment has more than one location for an Affy id, then the first location is taken. Currently, the hgu95av2MAP environment has only 9 Affy ids (out of 12625) that have more than one location and the hgu133aMAP environment has only 16 Affy ids (out of 22283) that have more than one location so this does not affect many identifiers.

Next any spaces are removed from each location as several locations have leading spaces.

Then a for loop (which is not efficient!) is used to look at each location individually and make a list that will be returned. A few particular strings are looked for in each location and these include `|' and `-'.

Locations that include `|' in the string are split based on the `|' as though it represents OR. For example, for Affy id, 32273\_at, in hgu95av2MAP the location is given as 5q33|5q31.1 and this function assumes this means 5q33 or 5q31.1 so it will return the values 5, 5q, 5q3, 5q33, 5q31, and 5q31.1 for this Affy id.

The `-' character is assumed to mean BETWEEN. For example, for Affy id, 1138\_at, in hgu95av2MAP the location is given as 2q11-q14 and this function assumes this means the location is somewhere between 2q11 and 2q14 so it will return the values 2, 2q, 2q1, 2q11, 2q12, 2q13, and 2q14 for this Affy id.

Now here is the first problem with this function. I do not know how to handle the `-' when the two strings are not of equal length. For example, for Affy id, 36779\_at, in hgu95av2MAP the location is given as 5q33.3-q34, but I do not know how to treat this BETWEEN because I do not know how many sub-bands there are between 5q33.3 and 5q34. Is there a 5q33.4 or 5q33.5, etc.? I'm not sure. So I treat this `-' as an `|'. This function will return the values 5, 5q, 5q3, 5q33, 5q33.3, and 5q34 for this Affy id and most likely, that is incorrect.

Another problem I have with the `-' occurs when all of the characters up until the last character do not match. For example, for Affy id, 38927\_i\_at, in hgu95av2MAP the location is given as 11q14-q21, but again I'm not sure how to treat this BETWEEN because I don't know the number of sub-bands between 11q14 and 11q21. Does 11q15 exist, etc.? So I again treat this `-' as an `|'. This function will return the values 11, 11q, 11q1, 11q14, 11q2, and 11q21 for this Affy id and this is probably incorrect. The problem with `-' also occurs when the location is something like 19cen-q13.1 for Affy id, 34670\_at, in hgu95av2MAP. Again I don't know the number of sub-bands between 19cen and 19q13.1 so I treat this BETWEEN as an OR.

Another problem I have with `cen' in the location is that sometimes the location looks like: 19p13.2-cen and very rarely it looks like: 5p13.1-5cen. In the second case, the chromosome number is included after the `-' and before the `cen'. This only occurs with the location 5p13.1-5cen in both hgu95av2MAP and hgu133aMAP and all other locations do not include the chromosome number after the `-'. Currently this function returns the wrong information for that one location. It will return the values 5, 5p, 5p1, 5p13, 5p13.1, 5p5,and 5p5cen, but it should return 5, 5p, 5p1, 5p13, 5p13.1, and 5cen so this one location is an error. All other locations that include `cen' are correct. For example, this function returns the values 19, 19p, 19p1, 19p13, 19p13.2, and 19cen for the location 19p13.2-cen.

This function is very slow because it contains for loops and thus, it would be useful to make it more efficient. Also, it would be nice at some point for someone with more knowledge on chromosome location figure out how to improve some of my string manipulation errors.

createLLChrCats is a wrapper that converts probe IDs to Entrez Gene IDs.

createMAPIncMat is a wrapper that calls createLLChrCats and then returns an incidence matrix with rows being the categories and cols the Entrez Gene IDs.

Examples

  library("hgu95av2.db")
  mapValues <- chrCats("hgu95av2")