rawCd4DnaseI           package:encoDnaseI           R Documentation

_A _d_a_t_a _f_r_a_m_e _w_i_t_h _i_n_f_o_r_m_a_t_i_o_n _o_n _t_h_e _U_C_S_C
_b_r_o_w_s_e_r _t_r_a_c_k _r_e_l_a_t_e_d _t_o _D_N_a_s_e_I _h_y_p_e_r_s_e_n_s_i_t_i_v_i_t_y

_D_e_s_c_r_i_p_t_i_o_n:

     A data frame with information on the UCSC browser track related to
     DNaseI hypersensitivity; the rawCD4 object is an eSet extension
     representing the same information; rawHelaDnaseI is like rawCD4
     but results on Hela cells.

_U_s_a_g_e:

     data(rawCd4DnaseI)
     data(rawHelaDnaseI)
     data(rawCD4)

_D_e_t_a_i_l_s:

     Obtained from a MySQL representation of the data  distributed at
     the Genome Browser FTP site

_V_a_l_u_e:

     a data.frame

_A_u_t_h_o_r(_s):

     Vince Carey <stvjc@channing.harvard.edu>

_R_e_f_e_r_e_n_c_e_s:

     <URL: hgdownload.cse.ucsc.edu> ... it appears that they do not
     offer the MYD/MYI representations, just the txt.gz and sql files
     now.   So if you obtain the encodeNhgriDnaseHsChipRawCd4.txt and
     .sql files at
     goldenPath/currentGenomes/Homo_Sapiens/encode/database, you can
     reconstruct the underlying data for this data.frame (hg18, Nov
     2007).

_E_x_a_m_p_l_e_s:

     data(rawCd4DnaseI)
     dim(rawCd4DnaseI)
     rawCd4DnaseI[1:5,]
     library(lattice)
     xyplot(dataValue~chromStart|chrom, data=rawCd4DnaseI, subset=chrom %in%
       c("chr1", "chr10", "chr19", "chr20"), scales=list(x=list(relation="free"))) 

