buildChromMap              package:reb              R Documentation

_A _f_u_n_c_t_i_o_n _t_o _g_e_n_e_r_a_t_e _a_n _i_n_s_t_a_n_t_i_a_t_i_o_n _o_f _a _c_h_r_o_m_L_o_c_a_t_i_o_n _c_l_a_s_s

_D_e_s_c_r_i_p_t_i_o_n:

     This function will take take the name of a data package and build
     a chromLocation object representing regions of the genomes.

_U_s_a_g_e:

     buildChromMap(dataPkg, regions)

_A_r_g_u_m_e_n_t_s:

 dataPkg: The name of the data package to be used (a.k.a generated by
          AnnBuilder or downloaded from Bioconductor web site

 regions: a character vector of genome regions to be generated

_D_e_t_a_i_l_s:

     This function is related to the buildChromLocation function found
     in the 'annotate' library. However, this function can be used to
     build specialized chromLocation objects based on gene mapping
     information.  For example, a chromLocation object can be build
     specifically for human chromosome 1 by supplying chromosomal band
     information, such as c("1p1", "1p2", "1p3", "1q1", "1q2", "1q3",
     "1q4").  Genes that map to these regions are isolated and a
     chromLocation object is returned. Note that genes are isolated by
     'grep'ing genome mapping information.  Therefore the number of
     genes that are able to placed into a defined genetic region (i.e.
     1q4) is dependent on the quality of the mapping information in the
     annotation data source.

     Unfortunately, not too many pre-built annotation packages are
     available for spotted arrays off the Bioconductor Metadata web
     set. Use AnnBuilder to make one or get one from your core.

_V_a_l_u_e:

     A 'chromLocation' object representing the specified genomic
     regions and annotation data source

_A_u_t_h_o_r(_s):

     Kyle A. Furge <kyle.furge@vai.org

_S_e_e _A_l_s_o:

     'buildChromLocation'

_E_x_a_m_p_l_e_s:

     ## 
     ## NOTE: This requires an annotation package to work.
     ##       In this example it is hu6800
     ## 
     if (require(hu6800)) {

       library(Biobase)
       library(annotate)

       ## Build a specific chrom arm

       chr1q <- buildChromMap("hu6800",c("1q1","1q2","1q3","1q4"))

       ## Build human data based on chrom arms

       data(Hs.arms) 
       map <- buildChromMap("hu6800",Hs.arms)
     }

