filters               package:exonmap               R Documentation

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

     Given a character vector of probeset names, filter it to keep (or
     exclude) those probesets that are mapped by X:Map to exons,
     introns, intergenic regions or are annotated as containing
     potentially cross-hybridizing (multitarget) probes. Functions of
     the form 'is. ...' return a logical vector.

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

       exonic(v,exclude=FALSE,mt.rm=TRUE)
       intronic(v,exclude=FALSE,mt.rm=TRUE)
       intergenic(v,exclude=FALSE,mt.rm=TRUE)
       multitarget(v,exclude=FALSE,mt.level=1)
       is.exonic(v)
       is.intronic(v)
       is.intergenic(v)
       is.multitarget(v,mt.level=1)
       select.probewise(v,filter=c("exonic","intronic","intergenic","multitarget"),mt.rm=TRUE,mt.level=1)
       exclude.probewise(v,filter=c("exonic","intronic","intergenic","multitarget"),mt.rm=TRUE,mt.level=1)

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

       v: A character vector of probeset names identifiers

 exclude: If TRUE, remove (rather than keep) matching probesets, from
          the list.

   mt.rm: If TRUE, remove multitarget probesets before returning the
          result

mt.level: The amount of multitargeting needed before a probeset is
          removed. See the package vignette for more details on how
          this number is calculated.

  filter: What sort of probeset should be retained/removed?

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

     Connects to the X:Map database to retrieve data. Before these
     functions can be used, 'xmapConnect' must have been called.

     By default, multitarget probesets are removed.

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

     A character vector of filtered names.

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

     C.J. Miller, M.J. Okoniewski

_R_e_f_e_r_e_n_c_e_s:

     <URL: http://xmap.picr.man.ac.uk>

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

     xmapConnect mappings details

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

       if(interactive()) {
         xmapConnect()
         gene <-  probeset.to.gene(c("3743919"))
         ps   <- gene.to.probeset(gene,as.vector=TRUE)
         exonic(ps)
         intronic(ps)
         intergenic(ps)
         multitarget(ps)
         exonic(ps,exclude=TRUE)
         intronic(ps,exclude=TRUE)
         intergenic(ps,exclude=TRUE)
         multitarget(ps,exclude=TRUE,mt.level=1)
         #or
         select.probewise(ps,"exonic") #etc..
         exclude.probewise(ps,"exonic") #etc..
         is.exonic(ps)
         is.intronic(ps)
         is.intergenic(ps)
         is.multitarget(ps)
         is.multitarget(ps,mt.level=4)

       }

